Is CCDC152 p.Ser96Arg (c.288T>A) pathogenic?

CCDC152 p.Ser96Arg (c.288T>A) is classified Uncertain significance in CCDC152 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-26). AlphaMissense: likely benign (0.214); Very rare (popmax 0.00752%, nfe).

How common is CCDC152 p.Ser96Arg (c.288T>A) in the general population?

CCDC152 p.Ser96Arg (c.288T>A) is very rare (popmax 0.00752%, nfe) (gnomAD).

What do computational predictors say about CCDC152 p.Ser96Arg (c.288T>A)?

AlphaMissense predicts likely benign (score 0.214) — an in-silico prediction, not a clinical call.

CCDC152 p.Ser96Arg

c.288T>A · rs1030664367 · VCV2215680

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.214 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00752%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.214	likely benign
REVEL	0.028	moderately benign-leaning
SaProt	LLR -8.56	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 2.1	GERP 1.8, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 41 kb · p 0.053 · regional, not allelic
Overall
CADD	19.23	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 0.00752% European (non-Finnish) · 84/1,117,104 alleles

Filtering AF 0.00621% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00571%

Overall 0.00586% 89/1,518,130 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00752%	13,299
Finnishnot grpmax-eligible	0.00334%	29,936
African / African-American	0.00277%	36,160
Remaining individualsnot grpmax-eligible	0.0017%	58,930

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: CCDC152
Protein: p.Ser96Arg
Coding: c.288T>A
MANE Select: NM_001134848
dbSNP: rs1030664367
Type: single nucleotide variant
Location: chr5:42779483 (GRCh38)
Gene constraint: LOEUF 1.871 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.17

Full CCDC152 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SELENOP p.Gly230= Benign ★★ same type
CCDC152 p.Ala116Asp Uncertain significance ★ ⚠ same type
CCDC152 p.Ala192Pro Uncertain significance ★ ⚠ same type
CCDC152 p.Ala228Glu Uncertain significance ★ ⚠ same type
CCDC152 p.Arg231His Uncertain significance ★ ⚠ same type
CCDC152 p.Arg253Trp Uncertain significance ★ ⚠ same type
CCDC152 p.Cys66Ser Uncertain significance ★ ⚠ same type
CCDC152 p.Cys8Tyr 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/ccdc152-p-ser96arg (accessed [today's date]).

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