COL7A1 p.Phe1238=
c.3714C>T · rs1380863838 · VCV513944
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00534%, 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 -2.1 | GERP -4.6 |
| Overall | ||
| CADD | 0.674 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,932 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00093%
15/1,613,472 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,733 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,238 |
| South Asian | 0.0022% | 45,545 |
| European (non-Finnish) | 0.000593% | 168,577 |
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
- COL7A1
- Protein
- p.Phe1238=
- Coding
- c.3714C>T
- MANE Select
- NM_000094
- dbSNP
- rs1380863838
- Type
- single nucleotide variant
- Location
- chr3:48586083 (GRCh38)
- Gene constraint
- LOEUF 0.69 · pLI <0.01 (gnomAD)
- Residue 1238
- the 'nonhelical region (nc1)' region
Similar variants
- COL7A1 c.1240+1G>T Likely pathogenic ★★ same type
- COL7A1 c.1637-1G>A Pathogenic/Likely pathogenic ★★ same type
- COL7A1 c.1906+1G>T Likely pathogenic ★★ same type
- COL7A1 c.2171-2A>G Likely pathogenic ★★ same type
- COL7A1 c.2587+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL7A1 c.2587+40G>A Pathogenic/Likely pathogenic ★★ same type
- COL7A1 c.266+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL7A1 c.266+2T>C Pathogenic/Likely pathogenic ★★ 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/col7a1-p-phe1238 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown