Is COL17A1 p.Pro31= (c.93A>G) pathogenic?

COL17A1 p.Pro31= (c.93A>G) is classified Benign/Likely benign in COL17A1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-02-24). Rare (popmax 0.691%, eas); Associated with junctional epidermolysis bullosa, non-Herlitz type.

What condition is associated with COL17A1 p.Pro31= (c.93A>G)?

COL17A1 p.Pro31= (c.93A>G) is associated with junctional epidermolysis bullosa, non-Herlitz type (ClinVar).

How common is COL17A1 p.Pro31= (c.93A>G) in the general population?

COL17A1 p.Pro31= (c.93A>G) is rare (popmax 0.691%, eas) (gnomAD).

COL17A1 p.Pro31=

c.93A>G · rs141808001 · VCV880159

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.691%, eas)

Conditions

junctional epidermolysis bullosa, non-Herlitz type

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 -4.6	GERP -4.2
Overall
CADD	4.188	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.691% East Asian · 310/44,864 alleles

Filtering AF 0.628% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.603%

Overall 0.0203% 327/1,614,120 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.691%	145
Remaining individualsnot grpmax-eligible	0.0144%	6,945
South Asian	0.00878%	11,385

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: COL17A1
Protein: p.Pro31=
Coding: c.93A>G
MANE Select: NM_000494
dbSNP: rs141808001
Type: single nucleotide variant
Location: chr10:104078546 (GRCh38)
Gene constraint: LOEUF 0.909 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 47.55 · 1 PDB
Residue 31: the 'nonhelical region (nc16)' region; the 'disordered' region

Full COL17A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

junctional epidermolysis bullosa, non-Herlitz type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COL17A1 p.Pro31Leu Uncertain significance ★ ⚠ same residue
COL17A1 p.Arg169Ter Pathogenic ★★ same condition
COL17A1 p.Arg72Ter Pathogenic/Likely pathogenic ★★ same condition
COL17A1 p.Arg9Ter Pathogenic ★★ same condition
COL17A1 p.Gly803Ter Pathogenic ★★ same condition
COL17A1 c.3277+3G>C Uncertain significance ★★ same condition
COL17A1 c.*115A>G Uncertain significance ★★ same condition
COL17A1 p.Ala253Val Uncertain significance ★★ ⚠ 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/col17a1-p-pro31 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown