COL4A6 p.Phe101=
c.303T>C · rs149820261 · VCV514998
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.96%, 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 5.4 | GERP -0.9, phastCons 1 |
| Overall | ||
| CADD | 9.189 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.96%
African / African-American · 2,257/57,011 alleles
Filtering AF
3.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.77%
Overall
0.223%
2,688/1,207,361 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.96% | 25 |
| Admixed American | 0.418% | 239 |
| Remaining individualsnot grpmax-eligible | 0.335% | 299 |
| Middle Eastern | 0.0921% | 1,086 |
| European (non-Finnish) | 0.00817% | 12,234 |
| South Asian | 0.00706% | 14,162 |
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.Phe101=
- Coding
- c.303T>C
- MANE Select
- NM_033641
- dbSNP
- rs149820261
- Type
- single nucleotide variant
- Location
- chrX:108219719 (GRCh38)
- Structure
- AlphaFold pLDDT 48.27
- Residue 101
- the 'triple-helical region' 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-phe101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown