COL4A6 p.Ser38=
c.114C>T · rs377506539 · VCV1259208
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0415%, eas)
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 2 | GERP 0.98, phastCons 0.98 |
| Overall | ||
| CADD | 7.696 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0415%
East Asian · 14/33,768 alleles
Filtering AF
0.025%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0201%
Overall
0.0019%
23/1,208,285 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0415% | 2,412 |
| Remaining individualsnot grpmax-eligible | 0.0168% | 5,940 |
| South Asian | 0.00177% | 56,488 |
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.Ser38=
- Coding
- c.114C>T
- MANE Select
- NM_033641
- dbSNP
- rs377506539
- Type
- single nucleotide variant
- Location
- chrX:108310778 (GRCh38)
- Structure
- AlphaFold pLDDT 48.27
- Residue 38
- the '7s domain' region
Similar variants
- 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
- COL4A6 c.3809-14G>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-ser38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown