Overview

Variant ID 29800
Entrez Gene ID 10457
Gene GPNMB (GeneCards)
Location hg19 7:23296615-23296615
hg38 7:23256996-23256996
Disease Autism Spectrum Disorders (view all the variants in this disease)
Method NextSeq500
Mutation(HGVS format) NC_000007.13:g.23296615 G>A (Genome Assembly: hg19)

Other information

Exon or Intron Exon
Position in protein NA
Amino acid changes in protein NA > NA
Position in cDNA NA
Changes in cDNA NA > NA
mRNA accession NA
mRNA length NA
Reference length 159138663

Annotations and predictions

MAF in gnomAD genome (version 2.0.1) 0
Variant IDs in COSMIC (version 89) 1312973
Variant occurences in COSMIC 2(urinary_tract)
EIGEN score 0.4955
CADD Raw score (version 1.3) 5.244748 (Deleterious)
FATHMM raw prediction score 0.96984 (Tolerated)
SIFT score 0.052 (Tolerated)
LRT score 0 (Deleterious)
MutationTaster score 1 (Deleterious)
MutatioinAssessor score 2.755 (Deleterious)
PROVEAN score -4.14 (Deleterious)
MetaSVM score -0.689 (Tolerated)
MetaLR score 0.187 (Tolerated)
MCAP score 0.036 (Deleterious)
FitCons score 0.625 (Highly Significant p < 0.003 )
Genomic Evolutionary Rate Profiling (GERP) score 5.23
PhyloP score based on multiple alignment of 100 vertebrates 8.53
PhastCons score based on multiple alignment of 100 vertebrates 1
SiPhy log transformed odds ratio on multiple alignment of 29 mammals 19.154
Deleterious probability by iFish2 0.8101 (Deleterious)
Deleterious probability by DeFine 0.9663 (Deleterious)
Entrez Gene ID 10457 (NCBI Gene)
Official Gene Symbol GPNMB (GeneCards)
Number of variants in GPNMB in this database 3 (view all the variants)
Full name glycoprotein nmb
Band 7p15.3
Other IDs Vega: OTTHUMG00000022811
OMIM: 604368
HGNC: HGNC:4462
Ensembl: ENSG00000136235
Other names NMB, HGFIN, PLCA3
Summary The protein encoded by this gene is a type I transmembrane glycoprotein which shows homology to the pMEL17 precursor, a melanocyte-specific protein. GPNMB shows expression in the lowly metastatic human melanoma cell lines and xenografts but does not show expression in the highly metastatic cell lines. GPNMB may be involved in growth delay and reduction of metastatic potential. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Individual #1

Individual ID 28867142.24 (view all the variants in this individual)
Pubmed ID 28867142
Whose mosaic mutation Male Patient  
Origin of mosaic mutation in patients de novo
Phenotype 3  
Disease Autism Spectrum Disorders (view all the variants in this disease)
OMIM ID 209850

Publication #1: 28867142

Pubmed ID 28867142
Title Exonic Mosaic Mutations Contribute Risk for Autism Spectrum Disorder
Journal American Journal of Human Genetics
Publication date 2017.08
Disease Autism Spectrum Disorders
Incidence 0.01
Number of cases cases of unknown sex: 247;