Is CCDC150 p.Cys97Phe (c.290G>T) pathogenic?

CCDC150 p.Cys97Phe (c.290G>T) is classified Uncertain significance in CCDC150 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-22). AlphaMissense: likely benign (0.322); Very rare (popmax 0.00577%, nfe).

How common is CCDC150 p.Cys97Phe (c.290G>T) in the general population?

CCDC150 p.Cys97Phe (c.290G>T) is very rare (popmax 0.00577%, nfe) (gnomAD).

What do computational predictors say about CCDC150 p.Cys97Phe (c.290G>T)?

AlphaMissense predicts likely benign (score 0.322) — an in-silico prediction, not a clinical call.

CCDC150 p.Cys97Phe

c.290G>T · VCV4220673

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.322 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00577%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.322	likely benign
REVEL	0.147	moderately benign-leaning
SaProt	LLR -5.88	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 4.2	GERP 1.4, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 93 kb · p 0.22 · regional, not allelic
Overall
CADD	22.4	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

Grpmax group 0.00577% European (non-Finnish) · 66/1,144,424 alleles

Filtering AF 0.00465% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00424%

Overall 0.00426% 67/1,571,508 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00577%	17,340
African / African-American	0.00134%	74,528

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: CCDC150
Protein: p.Cys97Phe
Coding: c.290G>T
MANE Select: NM_001080539
Type: single nucleotide variant
Location: chr2:196656746 (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-cys97phe (accessed [today's date]).

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