HSAN1C
MCID: NRP040
MIFTS: 35

Neuropathy, Hereditary Sensory and Autonomic, Type Ic (HSAN1C)

Categories: Cardiovascular diseases, Ear diseases, Eye diseases, Gastrointestinal diseases, Genetic diseases, Mental diseases, Metabolic diseases, Muscle diseases, Nephrological diseases, Neuronal diseases, Rare diseases, Skin diseases

Aliases & Classifications for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

MalaCards integrated aliases for Neuropathy, Hereditary Sensory and Autonomic, Type Ic:

Name: Neuropathy, Hereditary Sensory and Autonomic, Type Ic 57 13 73
Hereditary Sensory and Autonomic Neuropathy Type Ic 12 29 6
Neuropathy, Hereditary Sensory, Type Ic 57 29 6
Hsan1c 57 12 75
Hereditary Sensory and Autonomic Neuropathy Type 1c 12 15
Hsan Ic 57 75
Hsn Ic 57 75
Hsn1c 57 75
Neuropathy, Sensory and Autonomic, Hereditary, Type Ic 40
Neuropathy, Hereditary Sensory and Autonomic, 1c 75
Neuropathy, Hereditary Sensory, Type Ic; Hsn1c 57
Hereditary Sensory Neuropathy Type Ic 75

Characteristics:

OMIM:

57
Inheritance:
autosomal dominant

Miscellaneous:
variable age at onset (range first to third decade)


HPO:

32
neuropathy, hereditary sensory and autonomic, type ic:
Inheritance autosomal dominant inheritance


Classifications:



External Ids:

OMIM 57 613640
Disease Ontology 12 DOID:0070157
MedGen 42 C3150896
MeSH 44 D009477
UMLS 73 C3150896

Summaries for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

UniProtKB/Swiss-Prot : 75 Neuropathy, hereditary sensory and autonomic, 1C: A form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by prominent sensory abnormalities with a variable degree of motor and autonomic dysfunction. The neurological phenotype is often complicated by severe infections, osteomyelitis, and amputations. HSAN1C symptoms include loss of touch and vibration in the feet, dysesthesia and severe panmodal sensory loss in the upper and lower limbs, distal lower limb sensory loss with ulceration and osteomyelitis, and distal muscle weakness.

MalaCards based summary : Neuropathy, Hereditary Sensory and Autonomic, Type Ic, also known as hereditary sensory and autonomic neuropathy type ic, is related to neuropathy, hereditary sensory, type ie and neuropathy, and has symptoms including dysesthesia An important gene associated with Neuropathy, Hereditary Sensory and Autonomic, Type Ic is SPTLC2 (Serine Palmitoyltransferase Long Chain Base Subunit 2), and among its related pathways/superpathways are Sphingolipid metabolism and Sphingolipid signaling pathway. Affiliated tissues include skin and eye, and related phenotypes are abnormality of the foot and skin ulcer

Disease Ontology : 12 A hereditary sensory and autonomic neuropathy type 1 that has material basis in heterozygous mutation in the SPTLC2 gene on chromosome 14q24.

Description from OMIM: 613640

Related Diseases for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Graphical network of the top 20 diseases related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic:



Diseases related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Symptoms & Phenotypes for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Symptoms via clinical synopsis from OMIM:

57
Skin Nails Hair Skin:
anhidrosis
ulcers, distal, painless, due to sensory neuropathy

Skeletal Hands:
autoamputation
osteomyelitis or necrosis, distal, due to sensory neuropathy

Skeletal Feet:
foot deformities
autoamputation
osteomyelitis or necrosis, distal, due to sensory neuropathy

Neurologic Peripheral Nervous System:
distal sensory loss of all modalities (pain, temperature, touch, vibration)
distal limb muscular weakness due to peripheral neuropathy
lower limbs more affected than upper limbs
axonal sensorimotor neuropathy
dysesthesias


Clinical features from OMIM:

613640

Human phenotypes related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic:

32 (show all 10)
# Description HPO Frequency HPO Source Accession
1 abnormality of the foot 32 HP:0001760
2 skin ulcer 32 HP:0200042
3 osteomyelitis 32 HP:0002754
4 sensorimotor neuropathy 32 HP:0007141
5 anhidrosis 32 HP:0000970
6 distal muscle weakness 32 HP:0002460
7 distal sensory loss of all modalities 32 HP:0006984
8 distal sensory impairment 32 HP:0002936
9 dysesthesia 32 HP:0012534
10 autoamputation 32 HP:0001218

UMLS symptoms related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic:


dysesthesia

Drugs & Therapeutics for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Search Clinical Trials , NIH Clinical Center for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Genetic Tests for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Genetic tests related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic:

# Genetic test Affiliating Genes
1 Hereditary Sensory and Autonomic Neuropathy Type Ic 29 SPTLC2
2 Neuropathy, Hereditary Sensory, Type Ic 29

Anatomical Context for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

MalaCards organs/tissues related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic:

41
Skin, Eye

Publications for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Articles related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic:

# Title Authors Year
1
Clinical and metabolic consequences of L-serine supplementation in hereditary sensory and autonomic neuropathy type 1C. ( 29042446 )
2017

Variations for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

UniProtKB/Swiss-Prot genetic disease variations for Neuropathy, Hereditary Sensory and Autonomic, Type Ic:

75
# Symbol AA change Variation ID SNP ID
1 SPTLC2 p.Val359Met VAR_064798 rs267607090
2 SPTLC2 p.Gly382Val VAR_064799 rs267607089
3 SPTLC2 p.Ile504Phe VAR_064800 rs267607091
4 SPTLC2 p.Ala182Pro VAR_069525 rs864621998

ClinVar genetic disease variations for Neuropathy, Hereditary Sensory and Autonomic, Type Ic:

6 (show top 50) (show all 334)
# Gene Variation Type Significance SNP ID Assembly Location
1 SPTLC2 NM_004863.3(SPTLC2): c.1145G> T (p.Gly382Val) single nucleotide variant Likely pathogenic rs267607089 GRCh37 Chromosome 14, 78021674: 78021674
2 SPTLC2 NM_004863.3(SPTLC2): c.1145G> T (p.Gly382Val) single nucleotide variant Likely pathogenic rs267607089 GRCh38 Chromosome 14, 77555331: 77555331
3 SPTLC2 NM_004863.3(SPTLC2): c.1075G> A (p.Val359Met) single nucleotide variant Pathogenic rs267607090 GRCh37 Chromosome 14, 78021744: 78021744
4 SPTLC2 NM_004863.3(SPTLC2): c.1075G> A (p.Val359Met) single nucleotide variant Pathogenic rs267607090 GRCh38 Chromosome 14, 77555401: 77555401
5 SPTLC2 NM_004863.3(SPTLC2): c.544G> C (p.Ala182Pro) single nucleotide variant Pathogenic rs864621998 GRCh37 Chromosome 14, 78043197: 78043197
6 SPTLC2 NM_004863.3(SPTLC2): c.544G> C (p.Ala182Pro) single nucleotide variant Pathogenic rs864621998 GRCh38 Chromosome 14, 77576854: 77576854
7 SPTLC2 NM_004863.3(SPTLC2): c.768T> G (p.Ile256Met) single nucleotide variant Uncertain significance rs879254003 GRCh37 Chromosome 14, 78028821: 78028821
8 SPTLC2 NM_004863.3(SPTLC2): c.768T> G (p.Ile256Met) single nucleotide variant Uncertain significance rs879254003 GRCh38 Chromosome 14, 77562478: 77562478
9 SPTLC2 NM_004863.3(SPTLC2): c.851-5T> C single nucleotide variant Conflicting interpretations of pathogenicity rs199867946 GRCh37 Chromosome 14, 78023494: 78023494
10 SPTLC2 NM_004863.3(SPTLC2): c.851-5T> C single nucleotide variant Conflicting interpretations of pathogenicity rs199867946 GRCh38 Chromosome 14, 77557151: 77557151
11 SPTLC2 NM_004863.3(SPTLC2): c.*6080C> G single nucleotide variant Benign rs56040359 GRCh38 Chromosome 14, 77506204: 77506204
12 SPTLC2 NM_004863.3(SPTLC2): c.*6080C> G single nucleotide variant Benign rs56040359 GRCh37 Chromosome 14, 77972547: 77972547
13 SPTLC2 NM_004863.3(SPTLC2): c.*6018A> C single nucleotide variant Uncertain significance rs886050830 GRCh38 Chromosome 14, 77506266: 77506266
14 SPTLC2 NM_004863.3(SPTLC2): c.*6018A> C single nucleotide variant Uncertain significance rs886050830 GRCh37 Chromosome 14, 77972609: 77972609
15 SPTLC2 NM_004863.3(SPTLC2): c.*5989dupA duplication Likely benign rs149453307 GRCh38 Chromosome 14, 77506295: 77506295
16 SPTLC2 NM_004863.3(SPTLC2): c.*5989dupA duplication Likely benign rs149453307 GRCh37 Chromosome 14, 77972638: 77972638
17 SPTLC2 NM_004863.3(SPTLC2): c.*5531A> G single nucleotide variant Benign rs17105886 GRCh37 Chromosome 14, 77973096: 77973096
18 SPTLC2 NM_004863.3(SPTLC2): c.*5531A> G single nucleotide variant Benign rs17105886 GRCh38 Chromosome 14, 77506753: 77506753
19 SPTLC2 NM_004863.3(SPTLC2): c.*4948A> C single nucleotide variant Uncertain significance rs886050832 GRCh37 Chromosome 14, 77973679: 77973679
20 SPTLC2 NM_004863.3(SPTLC2): c.*4948A> C single nucleotide variant Uncertain significance rs886050832 GRCh38 Chromosome 14, 77507336: 77507336
21 SPTLC2 NM_004863.3(SPTLC2): c.*4645A> G single nucleotide variant Benign rs10132095 GRCh38 Chromosome 14, 77507639: 77507639
22 SPTLC2 NM_004863.3(SPTLC2): c.*4645A> G single nucleotide variant Benign rs10132095 GRCh37 Chromosome 14, 77973982: 77973982
23 SPTLC2 NM_004863.3(SPTLC2): c.*4402G> A single nucleotide variant Uncertain significance rs886050833 GRCh38 Chromosome 14, 77507882: 77507882
24 SPTLC2 NM_004863.3(SPTLC2): c.*4402G> A single nucleotide variant Uncertain significance rs886050833 GRCh37 Chromosome 14, 77974225: 77974225
25 SPTLC2 NM_004863.3(SPTLC2): c.*3612T> A single nucleotide variant Benign rs2364160 GRCh38 Chromosome 14, 77508672: 77508672
26 SPTLC2 NM_004863.3(SPTLC2): c.*3612T> A single nucleotide variant Benign rs2364160 GRCh37 Chromosome 14, 77975015: 77975015
27 SPTLC2 NM_004863.3(SPTLC2): c.*3396A> G single nucleotide variant Uncertain significance rs886050838 GRCh38 Chromosome 14, 77508888: 77508888
28 SPTLC2 NM_004863.3(SPTLC2): c.*3396A> G single nucleotide variant Uncertain significance rs886050838 GRCh37 Chromosome 14, 77975231: 77975231
29 SPTLC2 NM_004863.3(SPTLC2): c.*3034C> G single nucleotide variant Likely benign rs75977251 GRCh38 Chromosome 14, 77509250: 77509250
30 SPTLC2 NM_004863.3(SPTLC2): c.*3034C> G single nucleotide variant Likely benign rs75977251 GRCh37 Chromosome 14, 77975593: 77975593
31 SPTLC2 NM_004863.3(SPTLC2): c.*2936_*2938dupTGG duplication Likely benign rs200856836 GRCh38 Chromosome 14, 77509346: 77509348
32 SPTLC2 NM_004863.3(SPTLC2): c.*2936_*2938dupTGG duplication Likely benign rs200856836 GRCh37 Chromosome 14, 77975689: 77975691
33 SPTLC2 NM_004863.3(SPTLC2): c.*2699C> A single nucleotide variant Likely benign rs142877874 GRCh37 Chromosome 14, 77975928: 77975928
34 SPTLC2 NM_004863.3(SPTLC2): c.*2699C> A single nucleotide variant Likely benign rs142877874 GRCh38 Chromosome 14, 77509585: 77509585
35 SPTLC2 NM_004863.3(SPTLC2): c.*2338G> A single nucleotide variant Likely benign rs148034053 GRCh38 Chromosome 14, 77509946: 77509946
36 SPTLC2 NM_004863.3(SPTLC2): c.*2338G> A single nucleotide variant Likely benign rs148034053 GRCh37 Chromosome 14, 77976289: 77976289
37 SPTLC2 NM_004863.3(SPTLC2): c.*1936A> T single nucleotide variant Uncertain significance rs886050844 GRCh38 Chromosome 14, 77510348: 77510348
38 SPTLC2 NM_004863.3(SPTLC2): c.*1936A> T single nucleotide variant Uncertain significance rs886050844 GRCh37 Chromosome 14, 77976691: 77976691
39 SPTLC2 NM_004863.3(SPTLC2): c.*1457C> T single nucleotide variant Uncertain significance rs542322275 GRCh38 Chromosome 14, 77510827: 77510827
40 SPTLC2 NM_004863.3(SPTLC2): c.*1457C> T single nucleotide variant Uncertain significance rs542322275 GRCh37 Chromosome 14, 77977170: 77977170
41 SPTLC2 NM_004863.3(SPTLC2): c.*1193G> C single nucleotide variant Likely benign rs532533522 GRCh38 Chromosome 14, 77511091: 77511091
42 SPTLC2 NM_004863.3(SPTLC2): c.*1193G> C single nucleotide variant Likely benign rs532533522 GRCh37 Chromosome 14, 77977434: 77977434
43 SPTLC2 NM_004863.3(SPTLC2): c.*1014C> T single nucleotide variant Likely benign rs116563416 GRCh38 Chromosome 14, 77511270: 77511270
44 SPTLC2 NM_004863.3(SPTLC2): c.*1014C> T single nucleotide variant Likely benign rs116563416 GRCh37 Chromosome 14, 77977613: 77977613
45 SPTLC2 NM_004863.3(SPTLC2): c.*838G> A single nucleotide variant Uncertain significance rs760436119 GRCh38 Chromosome 14, 77511446: 77511446
46 SPTLC2 NM_004863.3(SPTLC2): c.*838G> A single nucleotide variant Uncertain significance rs760436119 GRCh37 Chromosome 14, 77977789: 77977789
47 SPTLC2 NM_004863.3(SPTLC2): c.*697C> G single nucleotide variant Likely benign rs187339967 GRCh38 Chromosome 14, 77511587: 77511587
48 SPTLC2 NM_004863.3(SPTLC2): c.*697C> G single nucleotide variant Likely benign rs187339967 GRCh37 Chromosome 14, 77977930: 77977930
49 SPTLC2 NM_004863.3(SPTLC2): c.*523C> T single nucleotide variant Likely benign rs561128453 GRCh38 Chromosome 14, 77511761: 77511761
50 SPTLC2 NM_004863.3(SPTLC2): c.*523C> T single nucleotide variant Likely benign rs561128453 GRCh37 Chromosome 14, 77978104: 77978104

Expression for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Search GEO for disease gene expression data for Neuropathy, Hereditary Sensory and Autonomic, Type Ic.

Pathways for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Pathways related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
11.36 SPTLC1 SPTLC2
2 10.7 SPTLC1 SPTLC2

GO Terms for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

Cellular components related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 endoplasmic reticulum GO:0005783 9.33 SPTLC1 SPTLC2 UCHL1
2 endoplasmic reticulum membrane GO:0005789 9.13 SPTLC1 SPTLC2 UCHL1
3 serine C-palmitoyltransferase complex GO:0017059 8.62 SPTLC1 SPTLC2

Biological processes related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 sphingolipid biosynthetic process GO:0030148 9.43 SPTLC1 SPTLC2
2 sphingolipid metabolic process GO:0006665 9.4 SPTLC1 SPTLC2
3 biosynthetic process GO:0009058 9.37 SPTLC1 SPTLC2
4 ceramide biosynthetic process GO:0046513 9.32 SPTLC1 SPTLC2
5 sphingosine biosynthetic process GO:0046512 9.26 SPTLC1 SPTLC2
6 sphingomyelin biosynthetic process GO:0006686 9.16 SPTLC1 SPTLC2
7 positive regulation of lipophagy GO:1904504 8.96 SPTLC1 SPTLC2
8 sphinganine biosynthetic process GO:0046511 8.62 SPTLC1 SPTLC2

Molecular functions related to Neuropathy, Hereditary Sensory and Autonomic, Type Ic according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 transferase activity, transferring acyl groups GO:0016746 9.16 SPTLC1 SPTLC2
2 pyridoxal phosphate binding GO:0030170 8.96 SPTLC1 SPTLC2
3 serine C-palmitoyltransferase activity GO:0004758 8.62 SPTLC1 SPTLC2

Sources for Neuropathy, Hereditary Sensory and Autonomic, Type Ic

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
Content
Loading form....