COL5A3 p.Phe178=
c.534C>T · rs114072683 · VCV768969
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.85%, afr)
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 2.6 | GERP -1, phastCons 0.51 |
| Overall | ||
| CADD | 5.336 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.85%
African / African-American · 1,392/75,042 alleles
Filtering AF
1.77%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.74%
Overall
0.0995%
1,606/1,614,164 alleles · low-frequency
exomes 799/1,461,842 · genomes 807/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.85% | 54 |
| Middle Eastern | 0.198% | 505 |
| Remaining individualsnot grpmax-eligible | 0.125% | 801 |
| Admixed American | 0.11% | 909 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,934 |
| South Asian | 0.00769% | 13,012 |
| European (non-Finnish) | 0.00381% | 26,223 |
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.Phe178=
- Coding
- c.534C>T
- MANE Select
- NM_015719
- dbSNP
- rs114072683
- Type
- single nucleotide variant
- Location
- chr19:10005618 (GRCh38)
- Gene constraint
- LOEUF 0.812 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.26
- Residue 178
- the laminin g-like domain
Similar variants
- COL5A3 p.Arg1177Trp Uncertain significance ★★ ⚠ same type
- COL5A3 p.Asp855= 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
- COL5A3 p.Ala121Thr 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-phe178 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown