Is CCDC24 p.Pro303Ser (c.907C>T) pathogenic?

CCDC24 p.Pro303Ser (c.907C>T) is classified Likely benign in CCDC24 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-08). AlphaMissense: likely benign (0.0623); Very rare (popmax 0.00308%, nfe).

How common is CCDC24 p.Pro303Ser (c.907C>T) in the general population?

CCDC24 p.Pro303Ser (c.907C>T) is very rare (popmax 0.00308%, nfe) (gnomAD).

What do computational predictors say about CCDC24 p.Pro303Ser (c.907C>T)?

AlphaMissense predicts likely benign (score 0.0623) — an in-silico prediction, not a clinical call.

CCDC24 p.Pro303Ser

c.907C>T · VCV3828569

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0623 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00308%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0623	likely benign
REVEL	0.02	moderately benign-leaning
SaProt	LLR -6.60	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 -0.79	GERP -1
Regional constraint	o/e 1.09	unconstrained · MANE · 4,278 bp · p 0.077 · regional, not allelic
Overall
CADD	0.634	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 0.00308% European (non-Finnish) · 36/1,169,778 alleles

Filtering AF 0.00225% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.002%

Overall 0.00232% 37/1,595,348 alleles · very rare exomes 34/1,443,102 · genomes 3/152,246 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00308%	32,494
African / African-American	0.00134%	74,442

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: CCDC24
Protein: p.Pro303Ser
Coding: c.907C>T
MANE Select: NM_152499
Type: single nucleotide variant
Location: chr1:43996143 (GRCh38)
Gene constraint: LOEUF 1.553 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.31
Residue 303: the 'disordered' region

Full CCDC24 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC24 p.Ala294Ser Uncertain significance ★ ⚠ same type
CCDC24 p.Ala305Thr Uncertain significance ★ ⚠ same type
CCDC24 p.Ala44Ser Uncertain significance ★ ⚠ same type
CCDC24 p.Arg178Lys Uncertain significance ★ ⚠ same type
CCDC24 p.Arg178Ser Uncertain significance ★ ⚠ same type
CCDC24 p.Arg22Cys Uncertain significance ★ ⚠ same type
CCDC24 p.Arg280Cys Uncertain significance ★ ⚠ same type
CCDC24 p.Arg280His 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/ccdc24-p-pro303ser (accessed [today's date]).

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