EDSSPD3
MCID: EHL083
MIFTS: 47

Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3 (EDSSPD3)

Categories: Bone diseases, Eye diseases, Fetal diseases, Genetic diseases, Metabolic diseases, Muscle diseases, Neuronal diseases, Rare diseases, Skin diseases

Aliases & Classifications for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

MalaCards integrated aliases for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3:

Name: Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3 57 72
Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like 57 29 13 6 39 70
Scd-Eds 57 58 72
Ehlers-Danlos Syndrome Spondylodysplastic Type 3 12 15
Edsspd3 57 72
Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like; Scd-Eds 57
Slc39a13-Related Spondylodysplastic Ehlers-Danlos Syndrome 58
Ehlers-Danlos Syndrome-Like Spondylocheirodysplasia 72
Spondylocheirodysplastic Ehlers-Danlos Syndrome 58
Slc39a13-Related Spondylodysplastic Eds 58
Slc39a13-Related Speds 58
Speds-Slc39a13 58

Characteristics:

Orphanet epidemiological data:

58
slc39a13-related spondylodysplastic ehlers-danlos syndrome
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide);

OMIM®:

57 (Updated 05-Apr-2021)
Miscellaneous:
waddling gait

Inheritance:
autosomal recessive


HPO:

31
ehlers-danlos syndrome, spondylodysplastic type, 3:
Inheritance autosomal recessive inheritance


Classifications:

Orphanet: 58  
Rare eye diseases
Rare systemic and rhumatological diseases
Rare bone diseases
Rare skin diseases
Developmental anomalies during embryogenesis


Summaries for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

UniProtKB/Swiss-Prot : 72 Ehlers-Danlos syndrome, spondylodysplastic type, 3: A form of Ehlers-Danlos syndrome, a group of connective tissue disorders characterized by skin hyperextensibility, articular hypermobility, and tissue fragility. EDSSPD3 is an autosomal recessive form characterized by a generalized skeletal dysplasia involving mainly the spine and striking clinical abnormalities of the hands, in addition to classic features of Ehlers-Danlos syndrome. Clinical features include postnatal growth retardation, moderate short stature, protuberant eyes with bluish sclerae, hands with finely wrinkled palms, atrophy of the thenar muscles, and tapering fingers. Radiologic features include mild to moderate platyspondyly, mild to moderate osteopenia of the spine, small ileum, flat proximal femoral epiphyses, short, wide femoral necks, and broad metaphyses (elbows, knees, wrists, and interphalangeal joints).

MalaCards based summary : Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3, also known as spondylocheirodysplasia, ehlers-danlos syndrome-like, is related to enteropathica and hypermanganesemia with dystonia 2, and has symptoms including waddling gait and joint laxity (elbow). An important gene associated with Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3 is SLC39A13 (Solute Carrier Family 39 Member 13), and among its related pathways/superpathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and NRF2 pathway. Affiliated tissues include eye and skin, and related phenotypes are failure to thrive and skeletal dysplasia

Disease Ontology : 12 An Ehlers-Danlos syndrome that has material basis in homozygous mutation in the zinc transporter gene SLC39A13 on chromosome 11p11 and that is characterized by short stature, hyperelastic skin and hypermobile joints, protuberant eyes with bluish sclerae, finely wrinkled palms, and characteristic radiologic features.

OMIM® : 57 Ehlers-Danlos syndrome spondylodysplastic type 3 is characterized by short stature, hyperelastic skin and hypermobile joints, protuberant eyes with bluish sclerae, finely wrinkled palms, and characteristic radiologic features (Giunta et al., 2008). For a discussion of genetic heterogeneity of the spondylodysplastic type of Ehlers-Danlos syndrome, see 130070. (612350) (Updated 05-Apr-2021)

Related Diseases for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Graphical network of the top 20 diseases related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3:



Diseases related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Symptoms & Phenotypes for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Human phenotypes related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3:

58 31 (show all 44)
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 failure to thrive 58 31 hallmark (90%) Very frequent (99-80%) HP:0001508
2 skeletal dysplasia 58 31 hallmark (90%) Very frequent (99-80%) HP:0002652
3 proptosis 58 31 hallmark (90%) Very frequent (99-80%) HP:0000520
4 bruising susceptibility 58 31 hallmark (90%) Very frequent (99-80%) HP:0000978
5 blue sclerae 58 31 hallmark (90%) Very frequent (99-80%) HP:0000592
6 hyperextensible skin 58 31 hallmark (90%) Very frequent (99-80%) HP:0000974
7 thin skin 58 31 hallmark (90%) Very frequent (99-80%) HP:0000963
8 moderately short stature 58 31 hallmark (90%) Very frequent (99-80%) HP:0008848
9 osteopenia 58 31 very rare (1%) Frequent (79-30%) HP:0000938
10 abnormality of the metaphysis 58 31 frequent (33%) Frequent (79-30%) HP:0000944
11 downslanted palpebral fissures 58 31 frequent (33%) Frequent (79-30%) HP:0000494
12 platyspondyly 58 31 frequent (33%) Frequent (79-30%) HP:0000926
13 tapered finger 58 31 frequent (33%) Frequent (79-30%) HP:0001182
14 absent palmar crease 58 31 frequent (33%) Frequent (79-30%) HP:0010489
15 broad femoral neck 58 31 frequent (33%) Frequent (79-30%) HP:0006429
16 short femoral neck 58 31 frequent (33%) Frequent (79-30%) HP:0100864
17 flat capital femoral epiphysis 58 31 frequent (33%) Frequent (79-30%) HP:0003370
18 thenar muscle atrophy 58 31 frequent (33%) Frequent (79-30%) HP:0003393
19 flexion contracture 58 31 occasional (7.5%) Occasional (29-5%) HP:0001371
20 depressed nasal bridge 31 very rare (1%) HP:0005280
21 hypertelorism 31 very rare (1%) HP:0000316
22 webbed neck 31 very rare (1%) HP:0000465
23 motor delay 31 very rare (1%) HP:0001270
24 kyphoscoliosis 31 very rare (1%) HP:0002751
25 bifid uvula 31 very rare (1%) HP:0000193
26 dislocated radial head 31 very rare (1%) HP:0003083
27 cigarette-paper scars 31 very rare (1%) HP:0001073
28 flared metaphysis 31 very rare (1%) HP:0003015
29 frontal bossing 31 HP:0002007
30 high palate 31 HP:0000218
31 dental malocclusion 31 HP:0000689
32 pes planus 31 HP:0001763
33 short stature 31 HP:0004322
34 waddling gait 31 HP:0002515
35 joint laxity 31 HP:0001388
36 delayed eruption of teeth 31 HP:0000684
37 hypodontia 31 HP:0000668
38 camptodactyly of finger 31 HP:0100490
39 short metacarpal 31 HP:0010049
40 short phalanx of finger 31 HP:0009803
41 flattened epiphysis 58 Frequent (79-30%)
42 irregular vertebral endplates 31 HP:0003301
43 prominent superficial veins 31 HP:0001015
44 joint contracture of the hand 31 HP:0009473

Symptoms via clinical synopsis from OMIM®:

57 (Updated 05-Apr-2021)
Head And Neck Mouth:
high palate
bifid uvula

Skeletal Feet:
pes planus

Head And Neck Eyes:
blue sclerae
downslanting palpebral fissures
protuberant eyes
corneal diameter, normal

Skeletal Hands:
thenar muscle atrophy
short metacarpals
short phalanges
finger contractures
small joint laxity
more
Skeletal Limbs:
joint laxity (elbow)
widened metaphyses (elbows and knees)

Growth Height:
short stature, moderate

Growth Weight:
birthweight at or below 3rd centile

Skeletal Spine:
osteopenia
platyspondyly
irregular endplates

Head And Neck Teeth:
delayed eruption of teeth
hypodontia
malocclusion

Skin Nails Hair Skin:
thin skin
cigarette-paper scars
easy bruisability
delayed wound healing
hyperelastic skin
more
Muscle Soft Tissue:
thenar muscle atrophy
hypothenar muscle atrophy

Skeletal Pelvis:
small ilia
short, wide femoral neck
mildly flattened proximal femoral epiphyses

Growth Other:
growth retardation, postnatal

Laboratory Abnormalities:
lysyl pyridinoline/hydroxylysyl pyridinoline (lp/hp) ratio approximately 1
normal lysyl hydroxylase activity
normal prolyl 4-hydroxylase activity

Clinical features from OMIM®:

612350 (Updated 05-Apr-2021)

UMLS symptoms related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3:


waddling gait; joint laxity (elbow)

GenomeRNAi Phenotypes related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3 according to GeneCards Suite gene sharing:

26 (show all 11)
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased shRNA abundance (Z-score < -2) GR00366-A-1 9.65 LGR6
2 Decreased shRNA abundance (Z-score < -2) GR00366-A-106 9.65 SLC39A10
3 Decreased shRNA abundance (Z-score < -2) GR00366-A-172 9.65 SLC39A10
4 Decreased shRNA abundance (Z-score < -2) GR00366-A-183 9.65 SLC39A10
5 Decreased shRNA abundance (Z-score < -2) GR00366-A-19 9.65 SLC30A1
6 Decreased shRNA abundance (Z-score < -2) GR00366-A-215 9.65 SLC39A10
7 Decreased shRNA abundance (Z-score < -2) GR00366-A-39 9.65 SLC39A10
8 Decreased shRNA abundance (Z-score < -2) GR00366-A-4 9.65 SLC39A10
9 Decreased shRNA abundance (Z-score < -2) GR00366-A-59 9.65 LGR6
10 Decreased shRNA abundance (Z-score < -2) GR00366-A-9 9.65 LGR6
11 shRNA abundance <= 50% GR00343-S 9.23 ENTPD1 HNF1A P4HB SLC30A4 SLC39A14 SLC39A6

MGI Mouse Phenotypes related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 cellular MP:0005384 10.18 CEBPB HNF1A KRT14 SLC30A2 SLC30A4 SLC39A10
2 homeostasis/metabolism MP:0005376 10.13 CEBPB ENTPD1 HNF1A KRT14 LOX P4HB
3 endocrine/exocrine gland MP:0005379 10.02 CEBPB HNF1A KRT14 P4HB SLC30A2 SLC30A4
4 mortality/aging MP:0010768 10 CEBPB HNF1A KRT14 LOX P4HB SLC30A1
5 integument MP:0010771 9.96 CEBPB HNF1A KRT14 LOX SLC30A2 SLC30A4
6 muscle MP:0005369 9.56 CEBPB ENTPD1 HNF1A LOX SLC39A14 SLC39A4
7 skeleton MP:0005390 9.28 CEBPB HNF1A LOX SLC30A4 SLC39A13 SLC39A14

Drugs & Therapeutics for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Search Clinical Trials , NIH Clinical Center for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Genetic Tests for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Genetic tests related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3:

# Genetic test Affiliating Genes
1 Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like 29 SLC39A13

Anatomical Context for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

MalaCards organs/tissues related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3:

40
Eye, Skin

Publications for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Articles related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3:

(show all 11)
# Title Authors PMID Year
1
Spondylocheiro dysplastic form of the Ehlers-Danlos syndrome--an autosomal-recessive entity caused by mutations in the zinc transporter gene SLC39A13. 57 6 61
18513683 2008
2
The zinc transporter SLC39A13/ZIP13 is required for connective tissue development; its involvement in BMP/TGF-beta signaling pathways. 57 6
18985159 2008
3
The Connective Tissue Disorder Associated with Recessive Variants in the SLC39A13 Zinc Transporter Gene (Spondylo-Dysplastic Ehlers-Danlos Syndrome Type 3): Insights from Four Novel Patients and Follow-Up on Two Original Cases. 61
32295219 2020
4
Zinc and Its Transporters in Epigenetics. 61
32274919 2020
5
Novel Nonsense Mutation in SLC39A13 Initially Presenting as Myopathy: Case Report and Review of the Literature. 61
29593477 2018
6
Changes in skin structure of the Zip13-KO mouse by Makomo (Zizania latifolia) feeding. 61
28781296 2017
7
ZIP13: A Study of Drosophila Offers an Alternative Explanation for the Corresponding Human Disease. 61
29445391 2017
8
Comparative study of dermal components and plasma TGF-β1 levels in Slc39a13/Zip13-KO mice. 61
26050750 2015
9
Molecular pathogenesis of spondylocheirodysplastic Ehlers-Danlos syndrome caused by mutant ZIP13 proteins. 61
25007800 2014
10
Spondylocheirodysplastic Ehlers-Danlos syndrome (SCD-EDS) and the mutant zinc transporter ZIP13. 61
26942106 2014
11
Promotion of vesicular zinc efflux by ZIP13 and its implications for spondylocheiro dysplastic Ehlers-Danlos syndrome. 61
23213233 2012

Variations for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

ClinVar genetic disease variations for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3:

6 (show top 50) (show all 55)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 SLC39A13 SLC39A13, 9-BP DEL, NT483 Deletion Pathogenic 2132 GRCh37:
GRCh38:
2 SLC39A13 NM_001128225.3(SLC39A13):c.221G>A (p.Gly74Asp) SNV Pathogenic 2133 rs121434363 GRCh37: 11:47431866-47431866
GRCh38: 11:47410315-47410315
3 SLC39A13 NM_001128225.3(SLC39A13):c.736A>G (p.Ile246Val) SNV Uncertain significance 469536 rs767784704 GRCh37: 11:47435976-47435976
GRCh38: 11:47414425-47414425
4 SLC39A13 NM_001128225.3(SLC39A13):c.635G>A (p.Arg212Gln) SNV Uncertain significance 469535 rs200490683 GRCh37: 11:47435048-47435048
GRCh38: 11:47413497-47413497
5 SLC39A13 NM_001128225.3(SLC39A13):c.149A>G (p.Asn50Ser) SNV Uncertain significance 835146 GRCh37: 11:47431794-47431794
GRCh38: 11:47410243-47410243
6 SLC39A13 NM_001128225.3(SLC39A13):c.1094T>C (p.Leu365Pro) SNV Uncertain significance 849736 GRCh37: 11:47436892-47436892
GRCh38: 11:47415341-47415341
7 SLC39A13 NM_001128225.3(SLC39A13):c.301+5G>A SNV Uncertain significance 860715 GRCh37: 11:47431951-47431951
GRCh38: 11:47410400-47410400
8 SLC39A13 NM_001128225.3(SLC39A13):c.487C>G (p.Leu163Val) SNV Uncertain significance 950842 GRCh37: 11:47433968-47433968
GRCh38: 11:47412417-47412417
9 SLC39A13 NM_001128225.3(SLC39A13):c.185G>C (p.Gly62Ala) SNV Uncertain significance 571538 rs1565660438 GRCh37: 11:47431830-47431830
GRCh38: 11:47410279-47410279
10 SLC39A13 NM_001128225.3(SLC39A13):c.265A>G (p.Ile89Val) SNV Uncertain significance 573374 rs754729494 GRCh37: 11:47431910-47431910
GRCh38: 11:47410359-47410359
11 SLC39A13 NM_001128225.3(SLC39A13):c.302-3T>C SNV Uncertain significance 653236 rs371414744 GRCh37: 11:47433474-47433474
GRCh38: 11:47411923-47411923
12 SLC39A13 NM_001128225.3(SLC39A13):c.139C>T (p.Arg47Cys) SNV Uncertain significance 663097 rs766701277 GRCh37: 11:47431784-47431784
GRCh38: 11:47410233-47410233
13 SLC39A13 NM_001128225.3(SLC39A13):c.1000G>A (p.Val334Met) SNV Uncertain significance 665369 rs1595887083 GRCh37: 11:47436670-47436670
GRCh38: 11:47415119-47415119
14 SLC39A13 NM_001128225.3(SLC39A13):c.767T>C (p.Leu256Pro) SNV Uncertain significance 537267 rs924156969 GRCh37: 11:47436007-47436007
GRCh38: 11:47414456-47414456
15 SLC39A13 NM_001128225.3(SLC39A13):c.35C>T (p.Ala12Val) SNV Uncertain significance 652451 rs556023069 GRCh37: 11:47431680-47431680
GRCh38: 11:47410129-47410129
16 SLC39A13 NM_001128225.3(SLC39A13):c.578A>G (p.Asn193Ser) SNV Uncertain significance 843758 GRCh37: 11:47434991-47434991
GRCh38: 11:47413440-47413440
17 SLC39A13 NM_001128225.3(SLC39A13):c.134C>T (p.Ala45Val) SNV Uncertain significance 844642 GRCh37: 11:47431779-47431779
GRCh38: 11:47410228-47410228
18 SLC39A13 NM_001128225.3(SLC39A13):c.571G>A (p.Ala191Thr) SNV Uncertain significance 391481 rs138998777 GRCh37: 11:47434984-47434984
GRCh38: 11:47413433-47413433
19 SLC39A13 NM_001128225.3(SLC39A13):c.403A>G (p.Ser135Gly) SNV Uncertain significance 450588 rs377518253 GRCh37: 11:47433578-47433578
GRCh38: 11:47412027-47412027
20 SLC39A13 NM_001128225.3(SLC39A13):c.95G>T (p.Gly32Val) SNV Uncertain significance 952775 GRCh37: 11:47431740-47431740
GRCh38: 11:47410189-47410189
21 SLC39A13 NM_001128225.3(SLC39A13):c.584G>A (p.Gly195Asp) SNV Uncertain significance 450596 rs750069673 GRCh37: 11:47434997-47434997
GRCh38: 11:47413446-47413446
22 SLC39A13 NM_001128225.3(SLC39A13):c.116G>A (p.Ser39Asn) SNV Uncertain significance 452270 rs775918761 GRCh37: 11:47431761-47431761
GRCh38: 11:47410210-47410210
23 SLC39A13 NM_001128225.3(SLC39A13):c.191G>A (p.Arg64Gln) SNV Uncertain significance 1008557 GRCh37: 11:47431836-47431836
GRCh38: 11:47410285-47410285
24 SLC39A13 NM_001128225.3(SLC39A13):c.38G>T (p.Gly13Val) SNV Uncertain significance 1010781 GRCh37: 11:47431683-47431683
GRCh38: 11:47410132-47410132
25 SLC39A13 NM_001128225.3(SLC39A13):c.1108G>A (p.Val370Met) SNV Uncertain significance 934628 GRCh37: 11:47436906-47436906
GRCh38: 11:47415355-47415355
26 SLC39A13 NM_001128225.3(SLC39A13):c.113G>A (p.Arg38Gln) SNV Uncertain significance 1019768 GRCh37: 11:47431758-47431758
GRCh38: 11:47410207-47410207
27 SLC39A13 NM_001128225.3(SLC39A13):c.589T>C (p.Cys197Arg) SNV Uncertain significance 1023087 GRCh37: 11:47435002-47435002
GRCh38: 11:47413451-47413451
28 SLC39A13 NM_001128225.3(SLC39A13):c.284C>T (p.Thr95Ile) SNV Uncertain significance 452914 rs1317018795 GRCh37: 11:47431929-47431929
GRCh38: 11:47410378-47410378
29 SLC39A13 NM_001128225.3(SLC39A13):c.255_269del (p.Leu87_Leu91del) Deletion Uncertain significance 838611 GRCh37: 11:47431898-47431912
GRCh38: 11:47410347-47410361
30 SLC39A13 NM_001128225.3(SLC39A13):c.833G>C (p.Ser278Thr) SNV Uncertain significance 948217 GRCh37: 11:47436374-47436374
GRCh38: 11:47414823-47414823
31 SLC39A13 NM_001128225.3(SLC39A13):c.640A>G (p.Ile214Val) SNV Uncertain significance 452828 rs750123189 GRCh37: 11:47435053-47435053
GRCh38: 11:47413502-47413502
32 SLC39A13 NM_001128225.3(SLC39A13):c.786+6C>T SNV Uncertain significance 284085 rs779162662 GRCh37: 11:47436032-47436032
GRCh38: 11:47414481-47414481
33 SLC39A13 NM_001128225.3(SLC39A13):c.118C>T (p.Arg40Trp) SNV Uncertain significance 651607 rs368796707 GRCh37: 11:47431763-47431763
GRCh38: 11:47410212-47410212
34 SLC39A13 NM_001128225.3(SLC39A13):c.55C>T (p.Leu19Phe) SNV Uncertain significance 597727 rs61995938 GRCh37: 11:47431700-47431700
GRCh38: 11:47410149-47410149
35 SLC39A13 NM_001128225.3(SLC39A13):c.991A>G (p.Ile331Val) SNV Uncertain significance 647707 rs1407619087 GRCh37: 11:47436661-47436661
GRCh38: 11:47415110-47415110
36 SLC39A13 NM_001128225.3(SLC39A13):c.615C>G (p.Pro205=) SNV Likely benign 469534 rs147495812 GRCh37: 11:47435028-47435028
GRCh38: 11:47413477-47413477
37 SLC39A13 NM_001128225.3(SLC39A13):c.539C>G (p.Ala180Gly) SNV Likely benign 197874 rs147227015 GRCh37: 11:47434952-47434952
GRCh38: 11:47413401-47413401
38 SLC39A13 NM_001128225.3(SLC39A13):c.651C>T (p.Ser217=) SNV Likely benign 513006 rs752707598 GRCh37: 11:47435153-47435153
GRCh38: 11:47413602-47413602
39 SLC39A13 NM_001128225.3(SLC39A13):c.795C>T (p.Asp265=) SNV Likely benign 515530 rs762829962 GRCh37: 11:47436336-47436336
GRCh38: 11:47414785-47414785
40 SLC39A13 NM_001128225.3(SLC39A13):c.646-7T>C SNV Likely benign 198279 rs140597965 GRCh37: 11:47435141-47435141
GRCh38: 11:47413590-47413590
41 SLC39A13 NM_001128225.3(SLC39A13):c.492G>T (p.Ala164=) SNV Likely benign 537268 rs149634596 GRCh37: 11:47433973-47433973
GRCh38: 11:47412422-47412422
42 SLC39A13 NM_001128225.3(SLC39A13):c.398C>T (p.Thr133Met) SNV Likely benign 196579 rs140574574 GRCh37: 11:47433573-47433573
GRCh38: 11:47412022-47412022
43 SLC39A13 NM_001128225.3(SLC39A13):c.439C>G (p.Gln147Glu) SNV Likely benign 287155 rs148291843 GRCh37: 11:47433920-47433920
GRCh38: 11:47412369-47412369
44 SLC39A13 NM_001128225.3(SLC39A13):c.406G>A (p.Ala136Thr) SNV Likely benign 706249 rs141246142 GRCh37: 11:47433581-47433581
GRCh38: 11:47412030-47412030
45 SLC39A13 NM_001128225.3(SLC39A13):c.1038G>A (p.Pro346=) SNV Likely benign 726453 rs772924353 GRCh37: 11:47436708-47436708
GRCh38: 11:47415157-47415157
46 SLC39A13 NM_001128225.3(SLC39A13):c.627C>T (p.Ala209=) SNV Likely benign 733090 rs768982611 GRCh37: 11:47435040-47435040
GRCh38: 11:47413489-47413489
47 SLC39A13 NM_001128225.3(SLC39A13):c.348A>G (p.Gly116=) SNV Likely benign 745727 rs202080209 GRCh37: 11:47433523-47433523
GRCh38: 11:47411972-47411972
48 SLC39A13 NM_001128225.3(SLC39A13):c.105G>A (p.Pro35=) SNV Likely benign 772490 rs1398817706 GRCh37: 11:47431750-47431750
GRCh38: 11:47410199-47410199
49 SLC39A13 NM_001128225.3(SLC39A13):c.696C>T (p.His232=) SNV Likely benign 772512 rs371961000 GRCh37: 11:47435198-47435198
GRCh38: 11:47413647-47413647
50 SLC39A13 NM_001128225.3(SLC39A13):c.78C>A (p.Leu26=) SNV Likely benign 469537 rs140844921 GRCh37: 11:47431723-47431723
GRCh38: 11:47410172-47410172

Expression for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Search GEO for disease gene expression data for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3.

Pathways for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Pathways related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.94 VCP SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14
2 11.66 SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14 SLC39A13
3
Show member pathways
11.3 SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14 SLC39A13

GO Terms for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

Cellular components related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 endoplasmic reticulum GO:0005783 9.8 VCP TMC8 SLC39A7 SLC39A6 SLC39A13 SLC30A1
2 integral component of membrane GO:0016021 9.77 TMC8 SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14
3 lysosomal membrane GO:0005765 9.46 SLC39A8 SLC39A14 SLC30A4 SLC30A2
4 integral component of plasma membrane GO:0005887 9.23 TMC8 SLC39A8 SLC39A6 SLC39A4 SLC39A14 SLC39A10

Biological processes related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3 according to GeneCards Suite gene sharing:

(show all 15)
# Name GO ID Score Top Affiliating Genes
1 ion transport GO:0006811 10.14 TMC8 SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14
2 transmembrane transport GO:0055085 10.11 VCP SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14
3 metal ion transport GO:0030001 9.8 SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14 SLC39A13
4 response to zinc ion GO:0010043 9.76 SLC39A13 SLC30A4 SLC30A2 KRT14
5 zinc ion transmembrane transport GO:0071577 9.76 SLC39A8 SLC39A7 SLC39A6 SLC39A14 SLC39A13 SLC30A4
6 zinc ion import across plasma membrane GO:0071578 9.72 SLC39A8 SLC39A6 SLC39A4 SLC39A14 SLC39A10
7 cation transport GO:0006812 9.7 SLC30A4 SLC30A2 SLC30A1
8 cadmium ion transmembrane transport GO:0070574 9.61 SLC39A8 SLC39A14 SLC30A1
9 cellular zinc ion homeostasis GO:0006882 9.56 SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14 SLC39A13
10 inorganic anion transport GO:0015698 9.55 SLC39A8 SLC39A14
11 manganese ion transmembrane transport GO:0071421 9.54 SLC39A8 SLC39A14
12 connective tissue development GO:0061448 9.51 SLC39A13 LOX
13 regulation of sequestering of zinc ion GO:0061088 9.49 SLC30A4 SLC30A2
14 zinc ion homeostasis GO:0055069 9.48 TMC8 SLC30A4
15 zinc ion transport GO:0006829 9.32 SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14 SLC39A13

Molecular functions related to Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 metal ion transmembrane transporter activity GO:0046873 9.5 SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14 SLC39A13
2 ubiquitin-like protein ligase binding GO:0044389 9.43 VCP CEBPB
3 iron ion transmembrane transporter activity GO:0005381 9.4 SLC39A8 SLC39A14
4 manganese ion transmembrane transporter activity GO:0005384 9.37 SLC39A8 SLC39A14
5 cation transmembrane transporter activity GO:0008324 9.33 SLC30A4 SLC30A2 SLC30A1
6 cadmium ion transmembrane transporter activity GO:0015086 9.32 SLC39A8 SLC39A14
7 zinc ion transmembrane transporter activity GO:0005385 9.32 SLC39A8 SLC39A7 SLC39A6 SLC39A4 SLC39A14 SLC39A13
8 anion:cation symporter activity GO:0015296 9.26 SLC39A8 SLC39A14

Sources for Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 05-Apr-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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