Is CCDC150 p.Ser969Pro (c.2905T>C) pathogenic?

CCDC150 p.Ser969Pro (c.2905T>C) is classified Uncertain significance in CCDC150 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-02). AlphaMissense: ambiguous (0.467); Absent from gnomAD v4.1.

How common is CCDC150 p.Ser969Pro (c.2905T>C) in the general population?

CCDC150 p.Ser969Pro (c.2905T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCDC150 p.Ser969Pro (c.2905T>C)?

AlphaMissense predicts ambiguous (score 0.467) — an in-silico prediction, not a clinical call.

CCDC150 p.Ser969Pro

c.2905T>C · VCV3996597

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.467 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.467	ambiguous
REVEL	0.196	benign-leaning
SaProt	LLR -13.61	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.87	GERP 0.66, phastCons 0.72
Regional constraint	o/e 1.03	unconstrained · MANE · 93 kb · p 0.22 · regional, not allelic
Overall
CADD	21.1	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

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: CCDC150
Protein: p.Ser969Pro
Coding: c.2905T>C
MANE Select: NM_001080539
Type: single nucleotide variant
Location: chr2:196730041 (GRCh38)
Gene constraint: LOEUF 1.112 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.19

Full CCDC150 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC150 p.Ala166Ser Uncertain significance ★ ⚠ same type
CCDC150 p.Ala166Thr Uncertain significance ★ ⚠ same type
CCDC150 p.Ala183Ser Uncertain significance ★ ⚠ same type
CCDC150 p.Ala419Glu Uncertain significance ★ ⚠ same type
CCDC150 p.Ala438Val Uncertain significance ★ ⚠ same type
CCDC150 p.Ala443Thr Uncertain significance ★ ⚠ same type
CCDC150 p.Ala454Pro Uncertain significance ★ ⚠ same type
CCDC150 p.Ala462Thr 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/ccdc150-p-ser969pro (accessed [today's date]).

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