Is CCDC152 p.Ala116Asp (c.347C>A) pathogenic?

CCDC152 p.Ala116Asp (c.347C>A) is classified Uncertain significance in CCDC152 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-05). AlphaMissense: likely benign (0.1382); Absent from gnomAD v4.1.

How common is CCDC152 p.Ala116Asp (c.347C>A) in the general population?

CCDC152 p.Ala116Asp (c.347C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCDC152 p.Ala116Asp (c.347C>A)?

AlphaMissense predicts likely benign (score 0.1382) — an in-silico prediction, not a clinical call.

CCDC152 p.Ala116Asp

c.347C>A · rs2530873190 · VCV2241472

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1382 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,344,486)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1382	likely benign
REVEL	0.036	moderately benign-leaning
SaProt	LLR -5.41	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 2.7	GERP 1.8, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 41 kb · p 0.053 · regional, not allelic
Overall
CADD	19.1	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

No allele count reported in gnomAD v4.1 (AN 1,344,486). 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: CCDC152
Protein: p.Ala116Asp
Coding: c.347C>A
MANE Select: NM_001134848
dbSNP: rs2530873190
Type: single nucleotide variant
Location: chr5:42783493 (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.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
CCDC152 p.Gln26Lys 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-ala116asp (accessed [today's date]).

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