Is C1QL3 p.Pro69Ser (c.205C>T) pathogenic?

C1QL3 p.Pro69Ser (c.205C>T) is classified Uncertain significance in C1QL3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-20). AlphaMissense: likely benign (0.0877); Absent from gnomAD v4.1.

How common is C1QL3 p.Pro69Ser (c.205C>T) in the general population?

C1QL3 p.Pro69Ser (c.205C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about C1QL3 p.Pro69Ser (c.205C>T)?

AlphaMissense predicts likely benign (score 0.0877) — an in-silico prediction, not a clinical call.

C1QL3 p.Pro69Ser

c.205C>T · VCV4647124

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0877 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,455,230)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0877	likely benign
REVEL	0.114	moderately benign-leaning
SaProt	LLR -10.00	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP -1.3, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 6,368 bp · p 0.003 · regional, not allelic
Overall
CADD	25.7	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

No allele count reported in gnomAD v4.1 (AN 1,455,230). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: C1QL3
Protein: p.Pro69Ser
Coding: c.205C>T
MANE Select: NM_001010908
Type: single nucleotide variant
Location: chr10:16520861 (GRCh38)
Gene constraint: LOEUF 0.788 · pLI 0.54 (gnomAD)
Structure: AlphaFold pLDDT 80.16
Residue 69: the collagen-like domain; the 'disordered' region

Full C1QL3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

C1QL3 p.Leu152= Benign ★★ same type
C1QL3 p.Ala40Val Uncertain significance ★ ⚠ same type
C1QL3 p.Arg98Pro Uncertain significance ★ ⚠ same type
C1QL3 p.Asn111Lys Uncertain significance ★ ⚠ same type
C1QL3 p.Asp48His Uncertain significance ★ ⚠ same type
C1QL3 p.Gln99Pro Uncertain significance ★ ⚠ same type
C1QL3 p.Glu23Lys Uncertain significance ★ ⚠ same type
C1QL3 p.Glu92Gln 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/c1ql3-p-pro69ser (accessed [today's date]).

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