COL4A2 p.Ala116=
c.348C>T · rs1223427718 · VCV2890192
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.6 | GERP -2.8 |
| Overall | ||
| CADD | 4.912 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/59,994 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000805%
13/1,614,006 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 29,997 |
| European (non-Finnish) | 0.000932% | 107,277 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- COL4A2
- Protein
- p.Ala116=
- Coding
- c.348C>T
- MANE Select
- NM_001846
- dbSNP
- rs1223427718
- Type
- single nucleotide variant
- Location
- chr13:110424985 (GRCh38)
- Gene constraint
- LOEUF 0.618 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.97 · 4 PDB
- Residue 116
- the 'disordered' region
Similar variants
- COL4A2 p.Ala116Val Uncertain significance ★ ⚠ same residue
- COL4A2 c.361-1G>A Pathogenic/Likely pathogenic ★★ same type
- COL4A2 p.Gly1389Arg Pathogenic/Likely pathogenic ★★ same type
- COL4A2 p.Gly619Asp Likely pathogenic ★★ same type
- COL4A2 c.2425+3G>A Uncertain significance ★★ same type
- COL4A2 c.315+5G>A Uncertain significance ★★ same type
- COL4A2 c.726+4A>G Uncertain significance ★★ same type
- COL4A2 p.Ala1183Val Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/col4a2-p-ala116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown