Is COL10A1 p.Pro492Ser (c.1474C>T) pathogenic?

COL10A1 p.Pro492Ser (c.1474C>T) is classified Uncertain significance in COL10A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-25). AlphaMissense: likely benign (0.0848); Very rare (popmax 0.00026%, nfe).

How common is COL10A1 p.Pro492Ser (c.1474C>T) in the general population?

COL10A1 p.Pro492Ser (c.1474C>T) is very rare (popmax 0.00026%, nfe) (gnomAD).

What do computational predictors say about COL10A1 p.Pro492Ser (c.1474C>T)?

AlphaMissense predicts likely benign (score 0.0848) — an in-silico prediction, not a clinical call.

COL10A1 p.Pro492Ser

c.1474C>T · rs769587032 · VCV2799890

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0848 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00026%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0848	likely benign
REVEL	0.644	pathogenic-leaning
SaProt	LLR -9.64	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.6	GERP 1, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 5,416 bp · p 0.14 · regional, not allelic
Overall
CADD	21.4	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00026% European (non-Finnish) · 3/1,155,458 alleles

Filtering AF 6.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000215% 3/1,396,018 alleles · very rare

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: COL10A1
Protein: p.Pro492Ser
Coding: c.1474C>T
MANE Select: NM_000493
dbSNP: rs769587032
Type: single nucleotide variant
Location: chr6:116120642 (GRCh38)
Gene constraint: LOEUF 0.855 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 58.80 · 1 PDB
Residue 492: the 'disordered' region; the 'triple-helical region' region

Full COL10A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COL10A1 p.Pro492Ala Uncertain significance ★★ ⚠ same residue
COL10A1 p.Arg71Ter Pathogenic/Likely pathogenic ★★ same type
COL10A1 p.Cys591Arg Likely pathogenic ★★ same type
COL10A1 p.Gln653Ter Pathogenic/Likely pathogenic ★★ same type
COL10A1 p.Gly18Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
COL10A1 p.Gly18Glu Pathogenic/Likely pathogenic ★★ ⚠ same type
COL10A1 p.Ser671Pro Pathogenic/Likely pathogenic ★★ same type
COL10A1 p.Tyr597His 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/col10a1-p-pro492ser (accessed [today's date]).

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