rs761819520
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_000091.5(COL4A3):c.997G>A(p.Gly333Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G333A) has been classified as Pathogenic.
Frequency
Consequence
NM_000091.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A3 | NM_000091.5 | c.997G>A | p.Gly333Arg | missense_variant | 18/52 | ENST00000396578.8 | |
MFF-DT | NR_102371.1 | n.1592+1566C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A3 | ENST00000396578.8 | c.997G>A | p.Gly333Arg | missense_variant | 18/52 | 1 | NM_000091.5 | P1 | |
MFF-DT | ENST00000439598.6 | n.1592+1566C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461446Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727068
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 11, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2020 | This variant has been observed in individual(s) with clinical features of Alport's syndrome (Invitae). ClinVar contains an entry for this variant (Variation ID: 585524). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant disrupts the p.Gly333 amino acid residue in COL4A3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 29089023). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant is present in population databases (rs761819520, ExAC 0.006%). This sequence change replaces glycine with arginine at codon 333 of the COL4A3 protein (p.Gly333Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine. - |
COL4A3-related disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 15, 2023 | The COL4A3 c.997G>A variant is predicted to result in the amino acid substitution p.Gly333Arg. The p.Gly333Arg residue is located in the conserved triple helical domain, where substitutions of the glycine are usually pathogenic (UniProt residues 43-1438, Hudson et al. 1993. PubMed ID: 8253711; https://www.ncbi.nlm.nih.gov/books/NBK21582/). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Another variant affecting the same amino acid residue, c.998G>A (p.Gly333Glu), has been reported in a large family Alport syndrome suggesting this amino acid is functionally important (Cervera-Acedo et al. 2017. PubMed ID: 29089023). This variant is interpreted as likely pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at