NPHLOP2
MCID: NPH042
MIFTS: 34

Nephrolithiasis/osteoporosis, Hypophosphatemic, 2 (NPHLOP2)

Categories: Bone diseases, Genetic diseases, Nephrological diseases

Aliases & Classifications for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

MalaCards integrated aliases for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2:

Name: Nephrolithiasis/osteoporosis, Hypophosphatemic, 2 57 72 29 13 6
Nephrolithiasis-Osteoporosis, Hypophosphatemic, 2 44 70
Hypophosphatemic Nephrolithiasis/osteoporosis 2 12 15
Nphlop2 57 72
Nephrolithiasis/osteoporosis, Hypophosphatemic, Type 2 39

Characteristics:

OMIM®:

57 (Updated 20-May-2021)
Inheritance:
autosomal dominant


HPO:

31
nephrolithiasis/osteoporosis, hypophosphatemic, 2:
Inheritance autosomal dominant inheritance


Classifications:



External Ids:

Disease Ontology 12 DOID:0080078
OMIM® 57 612287
OMIM Phenotypic Series 57 PS612286
MedGen 41 C2676782
UMLS 70 C2676782

Summaries for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

UniProtKB/Swiss-Prot : 72 Nephrolithiasis/osteoporosis, hypophosphatemic, 2: A disease characterized by decreased renal phosphate absorption, renal phosphate wasting, hypophosphatemia, hyperphosphaturia, hypercalciuria, nephrolithiasis and osteoporosis.

MalaCards based summary : Nephrolithiasis/osteoporosis, Hypophosphatemic, 2, also known as nephrolithiasis-osteoporosis, hypophosphatemic, 2, is related to cervical adenoma malignum and synchronous bilateral breast carcinoma. An important gene associated with Nephrolithiasis/osteoporosis, Hypophosphatemic, 2 is SLC9A3R1 (SLC9A3 Regulator 1), and among its related pathways/superpathways are PI3K-Akt signaling pathway and Integrated Cancer Pathway. Affiliated tissues include breast, and related phenotypes are osteopenia and hypophosphatemia

Disease Ontology : 12 A hypophosphatemic nephrolithiasis/osteoporosis that has material basis in heterozygous mutation in the SLC9A3R1 gene on chromosome 17q25.1.

More information from OMIM: 612287 PS612286

Related Diseases for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Diseases in the Hypophosphatemic Nephrolithiasis/osteoporosis family:

Nephrolithiasis/osteoporosis, Hypophosphatemic, 1 Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Diseases related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2 via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 30)
# Related Disease Score Top Affiliating Genes
1 cervical adenoma malignum 10.1 BRCA1 ATM
2 synchronous bilateral breast carcinoma 10.0 BRCA1 ATM
3 spinal muscular atrophy type 0 10.0 SMN2 SMN1
4 dysplastic nevus syndrome 10.0 BRCA1 ATM
5 spinal muscular atrophy, x-linked 2 10.0 SMN2 SMN1
6 familial ovarian cancer 10.0 BRCA1 ATM
7 autosomal recessive distal hereditary motor neuronopathy 10.0 SMN2 SMN1
8 proximal spinal muscular atrophy 10.0 SMN2 SMN1
9 spinal muscular atrophy, distal, autosomal recessive, 4 10.0 SMN2 SMN1
10 spinal muscular atrophy, distal, autosomal recessive, 1 10.0 SMN2 SMN1
11 punctate palmoplantar keratoderma 10.0 GJB2 BRCA1
12 dubowitz syndrome 10.0 SMN2 SMN1
13 x-linked nonsyndromic deafness 10.0 GJB2 COL4A5
14 spinal muscular atrophy with progressive myoclonic epilepsy 10.0 SMN2 SMN1
15 progressive muscular atrophy 10.0 SMN2 SMN1
16 pigmentary disorder, reticulate, with systemic manifestations, x-linked 10.0 BRCA1 ATM
17 childhood spinal muscular atrophy 9.9 SMN2 SMN1
18 spinal muscular atrophy, type iv 9.9 SMN2 SMN1
19 neuropathy, hereditary sensory and autonomic, type iii 9.9 SMN2 SMN1
20 spinal muscular atrophy, type ii 9.9 SMN2 SMN1
21 gm2-gangliosidosis, ab variant 9.8 HEXA GBA
22 chronic inflammatory demyelinating polyneuritis 9.8 SMN2 SMN1 HEXA
23 anterior horn cell disease 9.8 SMN2 SMN1 HEXA
24 spinal muscular atrophy 9.8 SMN2 SMN1 HEXA
25 gm1 gangliosidosis 9.7 HEXA GBA
26 bilateral breast cancer 9.7 BRCA1 ATM
27 gm2 gangliosidosis 9.6 SMN1 HEXA GBA
28 motor neuron disease 9.6 SMN2 SMN1 HEXA
29 neuromuscular disease 9.6 SMN2 SMN1 GJB2
30 tay-sachs disease 9.4 SMN2 SMN1 HEXA GBA

Graphical network of the top 20 diseases related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2:



Diseases related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Symptoms & Phenotypes for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Human phenotypes related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2:

31 (show all 7)
# Description HPO Frequency HPO Source Accession
1 osteopenia 31 HP:0000938
2 hypophosphatemia 31 HP:0002148
3 osteoporosis 31 HP:0000939
4 nephrolithiasis 31 HP:0000787
5 increased susceptibility to fractures 31 HP:0002659
6 hyperphosphaturia 31 HP:0003109
7 renal phosphate wasting 31 HP:0000117

Symptoms via clinical synopsis from OMIM®:

57 (Updated 20-May-2021)
Skeletal:
osteopenia
osteoporosis
increased susceptibility to fractures

Genitourinary Kidneys:
nephrolithiasis
renal phosphate wasting

Laboratory Abnormalities:
hypophosphatemia
hyperphosphaturia
increased serum 1,25-dihydroxyvitamin d

Skeletal Spine:
spinal deformity

Clinical features from OMIM®:

612287 (Updated 20-May-2021)

MGI Mouse Phenotypes related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 growth/size/body region MP:0005378 9.76 ATM BCKDHB BRCA1 COL4A5 GBA GJB2
2 mortality/aging MP:0010768 9.61 ATM BCKDHB BRCA1 COL4A5 GBA GJB2
3 nervous system MP:0003631 9.23 ATM BCKDHB BRCA1 GBA GJB2 HEXA

Drugs & Therapeutics for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Search Clinical Trials , NIH Clinical Center for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Cochrane evidence based reviews: nephrolithiasis-osteoporosis, hypophosphatemic, 2

Genetic Tests for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Genetic tests related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2:

# Genetic test Affiliating Genes
1 Nephrolithiasis/osteoporosis, Hypophosphatemic, 2 29 SLC9A3R1

Anatomical Context for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

MalaCards organs/tissues related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2:

40
Breast

Publications for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Articles related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2:

# Title Authors PMID Year
1
NHERF1 mutations and responsiveness of renal parathyroid hormone. 57 6
18784102 2008

Variations for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

ClinVar genetic disease variations for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2:

6
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 SLC9A3R1 NM_004252.5(SLC9A3R1):c.673G>A (p.Glu225Lys) SNV Pathogenic 5272 rs119486097 GRCh37: 17:72759575-72759575
GRCh38: 17:74763436-74763436
2 SLC9A3R1 NM_004252.5(SLC9A3R1):c.328C>G (p.Leu110Val) SNV Uncertain significance 5270 rs35910969 GRCh37: 17:72745313-72745313
GRCh38: 17:74749174-74749174
3 SLC9A3R1 NM_004252.5(SLC9A3R1):c.458G>A (p.Arg153Gln) SNV Uncertain significance 5271 rs41282065 GRCh37: 17:72758167-72758167
GRCh38: 17:74762028-74762028
4 SLC9A3R1 NM_004252.5(SLC9A3R1):c.657C>G (p.Ile219Met) SNV Uncertain significance 561111 rs147104235 GRCh37: 17:72759559-72759559
GRCh38: 17:74763420-74763420

UniProtKB/Swiss-Prot genetic disease variations for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2:

72
# Symbol AA change Variation ID SNP ID
1 SLC9A3R1 p.Leu110Val VAR_034899 rs35910969
2 SLC9A3R1 p.Arg153Gln VAR_048021 rs41282065
3 SLC9A3R1 p.Glu225Lys VAR_048022 rs119486097
4 SLC9A3R1 p.Glu68Ala VAR_067661 rs139622189

Expression for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Search GEO for disease gene expression data for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2.

Pathways for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Pathways related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.46 SLC9A3R1 COL4A5 BRCA1 ATM
2 11.07 BRCA1 ATM
3 11.01 BRCA1 ATM
4 10.76 BRCA1 ATM
5 10.62 BRCA1 ATM
6 10.23 BRCA1 ATM
7 9.88 HEXA GBA

GO Terms for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

Cellular components related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 SMN-Sm protein complex GO:0034719 9.16 SMN2 SMN1
2 Gemini of coiled bodies GO:0097504 8.96 SMN2 SMN1
3 SMN complex GO:0032797 8.62 SMN2 SMN1

Biological processes related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 response to ionizing radiation GO:0010212 9.48 BRCA1 ATM
2 intrinsic apoptotic signaling pathway in response to DNA damage GO:0008630 9.46 BRCA1 ATM
3 neuron apoptotic process GO:0051402 9.43 GBA ATM
4 glycosphingolipid metabolic process GO:0006687 9.4 HEXA GBA
5 spliceosomal snRNP assembly GO:0000387 9.37 SMN2 SMN1
6 spliceosomal complex assembly GO:0000245 9.32 SMN2 SMN1
7 import into nucleus GO:0051170 9.26 SMN2 SMN1
8 determination of adult lifespan GO:0008340 9.16 GBA ATM
9 DNA double-strand break processing GO:0000729 8.96 BRCA1 ATM
10 DNA-templated transcription, termination GO:0006353 8.62 SMN2 SMN1

Molecular functions related to Nephrolithiasis/osteoporosis, Hypophosphatemic, 2 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 identical protein binding GO:0042802 9.02 SMN2 SMN1 GJB2 BRCA1 ATM

Sources for Nephrolithiasis/osteoporosis, Hypophosphatemic, 2

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 20-May-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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