Gene Gene information from NCBI Gene database.
Entrez ID 4868
Gene name NPHS1 adhesion molecule, nephrin
Gene symbol NPHS1
Synonyms (NCBI Gene)
CNFNPHNnephrin
Chromosome 19
Chromosome location 19q13.12
Summary This gene encodes a member of the immunoglobulin family of cell adhesion molecules that functions in the glomerular filtration barrier in the kidney. The gene is primarily expressed in renal tissues, and the protein is a type-1 transmembrane protein found
SNPs SNP information provided by dbSNP.
144
SNP ID Visualize variation Clinical significance Consequence
rs28939695 C>T Likely-benign, conflicting-interpretations-of-pathogenicity, benign, pathogenic Coding sequence variant, missense variant
rs34124941 ->C Likely-pathogenic Frameshift variant, coding sequence variant
rs35238405 T>C Conflicting-interpretations-of-pathogenicity, benign Coding sequence variant, missense variant
rs114203578 C>G,T Likely-pathogenic Coding sequence variant, missense variant
rs114849139 C>G,T Benign, conflicting-interpretations-of-pathogenicity, likely-pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
261
miRTarBase ID miRNA Experiments Reference
MIRT676783 hsa-miR-125a-3p HITS-CLIP 23824327
MIRT676782 hsa-miR-764 HITS-CLIP 23824327
MIRT676781 hsa-miR-3934-5p HITS-CLIP 23824327
MIRT676780 hsa-miR-186-3p HITS-CLIP 23824327
MIRT676779 hsa-miR-150-5p HITS-CLIP 23824327
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
WT1 Unknown 15504938;23768159
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
31
GO ID Ontology Definition Evidence Reference
GO:0000165 Process MAPK cascade IEA
GO:0005515 Function Protein binding IPI 16525419, 21858180, 22662192
GO:0005886 Component Plasma membrane IBA
GO:0005886 Component Plasma membrane IDA 17464107
GO:0005886 Component Plasma membrane IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
602716 7908 ENSG00000161270
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O60500
Protein name Nephrin (Renal glomerulus-specific cell adhesion receptor)
Protein function Seems to play a role in the development or function of the kidney glomerular filtration barrier. Regulates glomerular vascular permeability. May anchor the podocyte slit diaphragm to the actin cytoskeleton. Plays a role in skeletal muscle format
PDB 4ZRT
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF07679 I-set 33 124 Immunoglobulin I-set domain Domain
PF08205 C2-set_2 138 228 CD80-like C2-set immunoglobulin domain Domain
PF08205 C2-set_2 242 328 CD80-like C2-set immunoglobulin domain Domain
PF08205 C2-set_2 344 428 CD80-like C2-set immunoglobulin domain Domain
PF08205 C2-set_2 444 538 CD80-like C2-set immunoglobulin domain Domain
PF08205 C2-set_2 548 634 CD80-like C2-set immunoglobulin domain Domain
PF13927 Ig_3 739 820 Domain
PF13927 Ig_3 838 924 Domain
PF00041 fn3 942 1025 Fibronectin type III domain Domain
Tissue specificity TISSUE SPECIFICITY: Specifically expressed in podocytes of kidney glomeruli.
Sequence
MALGTTLRASLLLLGLLTEGLAQLAIPASVPRGFWALPENLTVVEGASVELRCGVSTPGS
AVQWAKDGLLLGPDPRIPGFPRYRLEGDPARGEFHLHIEACDLSDDAEYECQVGRSEMGP
ELVS
PRVILSILVPPKLLLLTPEAGTMVTWVAGQEYVVNCVSGDAKPAPDITILLSGQTI
SDISANVNEGSQQKLFTVEATARVTPRSSDNRQLLVCEASSPALEAPI
KASFTVNVLFPP
GPPVIEWPGLDEGHVRAGQSLELPCVARGGNPLATLQWLKNGQPVSTAWGTEHTQAVARS
VLVMTVRPEDHGAQLSCEAHNSVSAGTQ
EHGITLQVTFPPSAIIILGSASQTENKNVTLS
CVSKSSRPRVLLRWWLGWRQLLPMEETVMDGLHGGHISMSNLTFLARREDNGLTLTCEAF
SEAFTKET
FKKSLILNVKYPAQKLWIEGPPEGQKLRAGTRVRLVCLAIGGNPEPSLMWYK
DSRTVTESRLPQESRRVHLGSVEKSGSTFSRELVLVTGPSDNQAKFTCKAGQLSASTQ
LA
VQFPPTNVTILANASALRPGDALNLTCVSVSSNPPVNLSWDKEGERLEGVAAPPRRAPFK
GSAAARSVLLQVSSRDHGQRVTCRAHSAELRETV
SSFYRLNVLYRPEFLGEQVLVVTAVE
QGEALLPVSVSANPAPEAFNWTFRGYRLSPAGGPRHRILSSGALHLWNVTRADDGLYQLH
CQNSEGTAEARLRLDVHYAPTIRALQDPTEVNVGGSVDIVCTVDANPILPGMFNWERLGE
DEEDQSLDDMEKISRGPTGRLRIHHAKLAQAGAYQCIVDN
GVAPPARRLLRLVVRFAPQV
EHPTPLTKVAAAGDSTSSATLHCRARGVPNIVFTWTKNGVPLDLQDPRYTEHTYHQGGVH
SSLLTIANVSAAQDYALFTCTATN
ALGSDQTNIQLVSISRPDPPSGLKVVSLTPHSVGLE
WKPGFDGGLPQRFCIRYEALGTPGFHYVDVVPPQATTFTLTGLQPSTRYRVWLLASNALG
DSGLA
DKGTQLPITTPGLHQPSGEPEDQLPTEPPSGPSGLPLLPVLFALGGLLLLSNASC
VGGVLWQRRLRRLAEGISEKTEAGSEEDRVRNEYEESQWTGERDTQSSTVSTTEAEPYYR
SLRDFSPQLPPTQEEVSYSRGFTGEDEDMAFPGHLYDEVERTYPPSGAWGPLYDEVQMGP
WDLHWPEDTYQDPRGIYDQVAGDLDTLEPDSLPFELRGHLV
Sequence length 1241
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Nephrin family interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
31
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Congenital and infantile nephrotic syndrome Likely pathogenic rs2513773078 RCV002306451
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital nephrotic syndrome Likely pathogenic; Pathogenic rs386833898, rs386833945, rs762392183 RCV001003824
RCV001003825
RCV001003823
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Finnish congenital nephrotic syndrome Likely pathogenic; Pathogenic rs143649022, rs1973073001, rs2146828046, rs771143648, rs1420623853, rs1568453378, rs753535989, rs753394912, rs2146819513, rs1973023048, rs2146821851, rs2146822164, rs2146828521, rs1242448684, rs2146816353
View all (295 more)
RCV002476714
RCV003469621
RCV003473899
RCV003405625
RCV003469739
View all (317 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Focal segmental glomerulosclerosis Likely pathogenic; Pathogenic rs753656470, rs138656762, rs386833865 RCV002294487
RCV001195706
RCV002294007
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Atypical hemolytic-uremic syndrome Conflicting classifications of pathogenicity; Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CONGENITAL NEPHROTIC SYNDROME, FINNISH TYPE ClinGen, GenCC, Orphanet
ClinGen, GenCC, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Corticosteroids response drug response ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Familial idiopathic steroid-resistant nephrotic syndrome Conflicting classifications of pathogenicity ClinVar
CTD
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Arthritis Infectious Infective arthritis Pubtator 18364044 Inhibit
★☆☆☆☆
Found in Text Mining only
Bright Disease Bright Disease CTD_human_DG 11337370, 20962747
★☆☆☆☆
Found in Text Mining only
Chromosome 22q11.2 Microduplication Syndrome Chromosome 22q11.2 microduplication syndrome Pubtator 31443662 Associate
★☆☆☆☆
Found in Text Mining only
Chronic kidney disease stage 5 Kidney Disease BEFREE 14570703, 15503167, 22732337, 27312921
★☆☆☆☆
Found in Text Mining only
Chronic Kidney Diseases Kidney Disease BEFREE 19520069
★☆☆☆☆
Found in Text Mining only
Chronic Kidney Diseases Kidney Disease GWASCAT_DG 29545352
★☆☆☆☆
Found in Text Mining only
Colon Carcinoma Colon Carcinoma BEFREE 24914378
★☆☆☆☆
Found in Text Mining only
Congenital nephrotic syndrome, Finnish type Congenital nephrotic syndrome Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Diabetes Diabetes BEFREE 18449463, 19746264
★☆☆☆☆
Found in Text Mining only
Diabetes Mellitus Diabetes mellitus Pubtator 15149332, 32099032 Inhibit
★☆☆☆☆
Found in Text Mining only