Is COL7A1 p.Ser698Arg (c.2094C>A) pathogenic?

COL7A1 p.Ser698Arg (c.2094C>A) is classified Uncertain significance in COL7A1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-14). AlphaMissense: likely benign (0.1878); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with COL7A1 p.Ser698Arg (c.2094C>A)?

COL7A1 p.Ser698Arg (c.2094C>A) is associated with Inborn genetic diseases (ClinVar).

How common is COL7A1 p.Ser698Arg (c.2094C>A) in the general population?

COL7A1 p.Ser698Arg (c.2094C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about COL7A1 p.Ser698Arg (c.2094C>A)?

AlphaMissense predicts likely benign (score 0.1878) — an in-silico prediction, not a clinical call.

COL7A1 p.Ser698Arg

c.2094C>A · VCV3684035

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1878 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1878	likely benign
REVEL	0.044	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>A here scores Δ0.39 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.4	GERP 0.067, phastCons 0.97
Regional constraint	o/e 0.84	unconstrained · MANE · 6,279 bp · p 1.1e-07 · regional, not allelic
Overall
CADD	15.04	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: COL7A1
Protein: p.Ser698Arg
Coding: c.2094C>A
MANE Select: NM_000094
Type: single nucleotide variant
Location: chr3:48589675 (GRCh38)
Gene constraint: LOEUF 0.69 · pLI <0.01 (gnomAD)
Residue 698: the 'nonhelical region (nc1)' region; the fibronectin type-iii 6 domain

Full COL7A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COL7A1 p.Ala1282Thr Uncertain significance ★★ ⚠ same condition
COL7A1 p.Ala2258Thr Uncertain significance ★★ ⚠ same condition
COL7A1 p.Ala2328Gly Uncertain significance ★★ same condition
COL7A1 p.Ala2513Val Uncertain significance ★★ ⚠ same condition
COL7A1 p.Ala2592Glu Uncertain significance ★★ same condition
COL7A1 p.Ala36Thr Uncertain significance ★★ same condition
COL7A1 p.Ala74Thr Uncertain significance ★★ ⚠ same condition
COL7A1 p.Ala74Val 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/col7a1-p-ser698arg (accessed [today's date]).

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