rs864309703
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3PP5
The NM_005267.5(GJA8):c.151G>A(p.Asp51Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
GJA8
NM_005267.5 missense
NM_005267.5 missense
Scores
8
9
2
Clinical Significance
Conservation
PhyloP100: 8.07
Genes affected
GJA8 (HGNC:4281): (gap junction protein alpha 8) This gene encodes a transmembrane connexin protein that is necessary for lens growth and maturation of lens fiber cells. The encoded protein is a component of gap junction channels and functions in a calcium and pH-dependent manner. Mutations in this gene have been associated with zonular pulverulent cataracts, nuclear progressive cataracts, and cataract-microcornea syndrome. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM1
In a topological_domain Extracellular (size 28) in uniprot entity CXA8_HUMAN there are 14 pathogenic changes around while only 0 benign (100%) in NM_005267.5
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.839
PP5
Variant 1-147908106-G-A is Pathogenic according to our data. Variant chr1-147908106-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 217355.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=3}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJA8 | NM_005267.5 | c.151G>A | p.Asp51Asn | missense_variant | 2/2 | ENST00000369235.2 | NP_005258.2 | |
GJA8 | XM_011509417.3 | c.151G>A | p.Asp51Asn | missense_variant | 1/2 | XP_011507719.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GJA8 | ENST00000369235.2 | c.151G>A | p.Asp51Asn | missense_variant | 2/2 | NM_005267.5 | ENSP00000358238 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 35
GnomAD4 exome
Cov.:
35
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:5Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Cataract 1 multiple types Pathogenic:3Uncertain:1
Pathogenic, criteria provided, single submitter | clinical testing | 3billion | Jan 03, 2022 | The variant has been previously reported as de novo in a similarly affected individual (PMID: 26694549, PS2_S) A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000521485,VCV000574353, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.787, PP3_P). A missense variant is a common mechanism associated with Cataract 1 (PP2_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M).Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. - |
Uncertain significance, criteria provided, single submitter | curation | Dept. Genetics and Cancer, Menzies Institute for Medical Research, University of Tasmania | Jan 21, 2023 | Variant identified and curated during a GJA8 specific review of the literature in relation to pediatric or congenital cataract. ACMG-AMP criteria applied: PS4(Supporting), PM1(Supporting), PM2(Supporting), PM6(Supporting), PP3. Original variant report: PMID:26694549;29464339. Additional phenotype/s reported in these individual/s are: Microphthalmia, unilateral sclerocornea. Microphthalmia, anterior segment dysgenesis, persistent pupillary membrane. Microphthalmia, deep set eyes, corneal leukoma, buphthalmos, corectopia, nystagmus. Gene review and curation guidelines are outlined in: https://doi.org/10.1080/17469899.2023.2160320 - |
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 10, 2021 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 17, 2023 | For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Asp51 amino acid residue in GJA8. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GJA8 protein function. ClinVar contains an entry for this variant (Variation ID: 217355). This missense change has been observed in individual(s) with autosomal dominant cataract (PMID: 26694549, 29464339). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 51 of the GJA8 protein (p.Asp51Asn). - |
acorea-microphthalmia-cataract syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | UOEH Ophthalmology lab, University Of Occupational And Environmental Health, Japan | Jul 07, 2023 | It provides a new screening target for prenatal diagnosis of familial acorea. - |
Developmental cataract Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Eye Genetics Research Group, Children's Medical Research Institute | Jan 09, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D
REVEL
Pathogenic
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of glycosylation at S50 (P = 0.1682);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at