COL7A1 p.Pro180=
c.540T>A · rs1473537751 · VCV796789
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00445%, eas)
Conditions
1
epidermolysis bullosa dystrophica
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 -11 | GERP -3.4 |
| Overall | ||
| CADD | 0.145 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00445%
East Asian · 2/44,900 alleles
Filtering AF
0.000738%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000124%
2/1,614,024 alleles · very rare
exomes 1/1,461,862 · genomes 1/152,162 · joint denominator
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.Pro180=
- Coding
- c.540T>A
- MANE Select
- NM_000094
- dbSNP
- rs1473537751
- Type
- single nucleotide variant
- Location
- chr3:48593244 (GRCh38)
- Gene constraint
- LOEUF 0.69 · pLI <0.01 (gnomAD)
- Residue 180
- the 'nonhelical region (nc1)' region; the vwfa 1 domain
Similar variants
- COL7A1 p.Pro180His Uncertain significance ★ ⚠ same residue
- COL7A1 c.1637-1G>A Pathogenic/Likely pathogenic ★★ same condition
- COL7A1 c.2587+1G>A Pathogenic/Likely pathogenic ★★ same condition
- COL7A1 c.2587+40G>A Pathogenic/Likely pathogenic ★★ same condition
- COL7A1 c.266+1G>A Pathogenic/Likely pathogenic ★★ same condition
- COL7A1 c.2710+2T>C Pathogenic/Likely pathogenic ★★ same condition
- COL7A1 c.2992+2T>G Pathogenic ★★ same condition
- COL7A1 c.2993-2A>G Likely pathogenic ★★ 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/col7a1-p-pro180 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown