COL6A6 p.Arg804=
c.2412G>T · rs149727307 · VCV782432
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.45%, 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 1.1 | GERP -0.36, phastCons 1 |
| Overall | ||
| CADD | 3.209 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.45%
African / African-American · 1,088/74,938 alleles
Filtering AF
1.38%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.35%
Overall
0.0763%
1,229/1,610,294 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.45% | 69 |
| Remaining individualsnot grpmax-eligible | 0.106% | 944 |
| Admixed American | 0.0935% | 1,069 |
| Middle Eastern | 0.0662% | 1,511 |
| South Asian | 0.00552% | 18,106 |
| European (non-Finnish) | 0.000849% | 117,758 |
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
- COL6A6
- Protein
- p.Arg804=
- Coding
- c.2412G>T
- MANE Select
- NM_001102608
- dbSNP
- rs149727307
- Type
- single nucleotide variant
- Location
- chr3:130570828 (GRCh38)
- Gene constraint
- LOEUF 1.043 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.61
- Residue 804
- the 'nonhelical region' region
Similar variants
- COL6A6 p.Arg804Gln Uncertain significance ★ ⚠ same residue
- COL6A6 p.Arg804Trp Uncertain significance ★ ⚠ same residue
- COL6A6 p.Arg1295Ter Uncertain significance ★★ same type
- COL6A6 p.Arg1864Thr Uncertain significance ★★ same type
- COL6A6 p.Arg906His Uncertain significance ★★ ⚠ same type
- COL6A6 p.Arg937Trp Uncertain significance ★★ ⚠ same type
- COL6A6 p.Tyr1805Cys Uncertain significance ★★ ⚠ same type
- COL6A6 c.2977+4A>T Benign ★★ 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/col6a6-p-arg804 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown