rs397514704
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_021954.4(GJA3):c.616T>A(p.Phe206Ile) 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F206L) has been classified as Uncertain significance.
Frequency
Consequence
NM_021954.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJA3 | NM_021954.4 | c.616T>A | p.Phe206Ile | missense_variant | 2/2 | ENST00000241125.4 | |
GJA3 | XM_011535048.3 | c.616T>A | p.Phe206Ile | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJA3 | ENST00000241125.4 | c.616T>A | p.Phe206Ile | missense_variant | 2/2 | 3 | NM_021954.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 35
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Cataract 14 multiple types Pathogenic:1Uncertain:1
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 GJA3 specific review of the literature in relation to pediatric or congenital cataract. ACMG-AMP criteria applied: PM2(Supporting), PP1, PP3. Original variant report: PMID:22550389. The cataract phenotype reported for this variant is: Nuclear. Gene review and curation guidelines are outlined in: https://doi.org/10.1080/17469899.2023.2160320 - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at