Is COL19A1 p.Pro970Ser (c.2908C>T) pathogenic?

COL19A1 p.Pro970Ser (c.2908C>T) is classified Uncertain significance in COL19A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-26). AlphaMissense: likely benign (0.1102); Absent from gnomAD v4.1.

How common is COL19A1 p.Pro970Ser (c.2908C>T) in the general population?

COL19A1 p.Pro970Ser (c.2908C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about COL19A1 p.Pro970Ser (c.2908C>T)?

AlphaMissense predicts likely benign (score 0.1102) — an in-silico prediction, not a clinical call.

COL19A1 p.Pro970Ser

c.2908C>T · VCV4655477

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1102 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1102	likely benign
REVEL	0.482	indeterminate
SaProt	LLR -8.70	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP 1.5, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 328 kb · p 0.71 · regional, not allelic
Overall
CADD	24.2	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: COL19A1
Protein: p.Pro970Ser
Coding: c.2908C>T
MANE Select: NM_001858
Type: single nucleotide variant
Location: chr6:70188126 (GRCh38)
Gene constraint: LOEUF 0.876 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 55.83
Residue 970: the collagen-like 11 domain; the 'disordered' region; the 'triple-helical region 5 (col5)' region

Full COL19A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COL19A1 p.Ala1046Thr Uncertain significance ★ ⚠ same type
COL19A1 p.Ala1101Val Uncertain significance ★ ⚠ same type
COL19A1 p.Ala1110Thr Uncertain significance ★ ⚠ same type
COL19A1 p.Ala148Asp Uncertain significance ★ ⚠ same type
COL19A1 p.Ala193Val Uncertain significance ★ ⚠ same type
COL19A1 p.Ala238Pro Uncertain significance ★ ⚠ same type
COL19A1 p.Ala277Gly Uncertain significance ★ ⚠ same type
COL19A1 p.Ala294Thr 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/col19a1-p-pro970ser (accessed [today's date]).

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