COL4A6 p.Pro1179=
c.3537G>A · rs144803723 · VCV594995
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.428%, afr)
Conditions
1
hearing loss, X-linked 6
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 0.45 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 7.587 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.428%
African / African-American · 242/56,580 alleles
Filtering AF
0.383%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.366%
Overall
0.0325%
386/1,188,987 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.428% | 234 |
| Admixed American | 0.0387% | 2,583 |
| Remaining individualsnot grpmax-eligible | 0.0257% | 3,898 |
| European (non-Finnish) | 0.013% | 7,681 |
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
- COL4A6
- Protein
- p.Pro1179=
- Coding
- c.3537G>A
- MANE Select
- NM_033641
- dbSNP
- rs144803723
- Type
- single nucleotide variant
- Location
- chrX:108169973 (GRCh38)
- Structure
- AlphaFold pLDDT 48.27
- Residue 1179
- the 'triple-helical region' region
Similar variants
- COL4A6 p.Pro1179Leu Uncertain significance ★ ⚠ same residue
- COL4A6 p.Arg1269Ter Uncertain significance ★★ same condition
- COL4A6 p.Gly1484Arg Uncertain significance ★★ ⚠ same condition
- COL4A6 c.2132-6G>A Benign/Likely benign ★★ same condition
- COL4A6 c.2132-6G>T Benign/Likely benign ★★ same condition
- COL4A6 c.2956+39G>A Benign ★★ same condition
- COL4A6 c.3138+17C>T Benign/Likely benign ★★ same condition
- COL4A6 c.3139-4G>A Benign/Likely benign ★★ same condition
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/col4a6-p-pro1179 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown