Is COL20A1 p.Asp232Glu (c.696C>A) pathogenic?

COL20A1 p.Asp232Glu (c.696C>A) is classified Uncertain significance in COL20A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-06). AlphaMissense: likely benign (0.261); Absent from gnomAD v4.1.

How common is COL20A1 p.Asp232Glu (c.696C>A) in the general population?

COL20A1 p.Asp232Glu (c.696C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about COL20A1 p.Asp232Glu (c.696C>A)?

AlphaMissense predicts likely benign (score 0.261) — an in-silico prediction, not a clinical call.

COL20A1 p.Asp232Glu

c.696C>A · VCV4005150

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.261 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.261	likely benign
REVEL	0.146	moderately benign-leaning
SaProt	LLR -3.88	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.064	GERP -3.4, phastCons 0.93
Regional constraint	o/e 1.07	unconstrained · MANE · 35 kb · p 0.0022 · regional, not allelic
Overall
CADD	15.6	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: COL20A1
Protein: p.Asp232Glu
Coding: c.696C>A
MANE Select: NM_020882
Type: single nucleotide variant
Location: chr20:63308011 (GRCh38)
Gene constraint: LOEUF 1.419 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.88 · 4 PDB
Residue 232: the vwfa domain

Full COL20A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COL20A1 p.Thr141= Benign ★★ same type
COL20A1 p.Ala1059Pro Uncertain significance ★ ⚠ same type
COL20A1 p.Ala1063Thr Uncertain significance ★ ⚠ same type
COL20A1 p.Ala1244Ser Uncertain significance ★ ⚠ same type
COL20A1 p.Ala1265Thr Uncertain significance ★ ⚠ same type
COL20A1 p.Ala274Thr Uncertain significance ★ ⚠ same type
COL20A1 p.Ala300Thr Uncertain significance ★ ⚠ same type
COL20A1 p.Ala312Thr Uncertain significance ★ ⚠ 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/col20a1-p-asp232glu (accessed [today's date]).

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