COL5A3 p.Val571=
c.1713G>A · VCV4232365
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0626%, sas)
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 -0.99 | GERP -0.77 |
| Overall | ||
| CADD | 7.574 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0626%
South Asian · 57/91,082 alleles
Filtering AF
0.0496%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0449%
Overall
0.00502%
81/1,614,068 alleles · ultra-rare
exomes 80/1,461,862 · genomes 1/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0626% | 1,598 |
| Middle Eastern | 0.0164% | 6,084 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| European (non-Finnish) | 0.00169% | 59,002 |
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
- COL5A3
- Protein
- p.Val571=
- Coding
- c.1713G>A
- MANE Select
- NM_015719
- Type
- single nucleotide variant
- Location
- chr19:9993416 (GRCh38)
- Gene constraint
- LOEUF 0.812 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.26
- Residue 571
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL5A3 p.Arg1177Trp Uncertain significance ★★ ⚠ same type
- COL5A3 p.Asp855= Benign ★★ same type
- COL5A3 p.Phe178= Benign ★★ same type
- COL5A3 p.Pro1050Ser Benign ★★ same type
- COL5A3 p.Pro496= Likely benign ★★ same type
- COL5A3 p.Val1195Ala Benign ★★ same type
- COL5A3 p.Ala1005Thr Uncertain significance ★ ⚠ same type
- COL5A3 p.Ala1096Thr 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/col5a3-p-val571 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown