Is CC2D2A p.Val975Asp (c.2924T>A) pathogenic?

CC2D2A p.Val975Asp (c.2924T>A) is classified Uncertain significance in CC2D2A (ClinVar, Single submitter, 1 submitter; last evaluated 2017-09-07). AlphaMissense: likely pathogenic (0.8846); Absent from gnomAD v4.1.

How common is CC2D2A p.Val975Asp (c.2924T>A) in the general population?

CC2D2A p.Val975Asp (c.2924T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CC2D2A p.Val975Asp (c.2924T>A)?

AlphaMissense predicts likely pathogenic (score 0.8846) — an in-silico prediction, not a clinical call.

CC2D2A p.Val975Asp

c.2924T>A · rs1560183164 · VCV593777

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8846 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8846	likely pathogenic · top 8% in CC2D2A
REVEL	0.851	moderately pathogenic-leaning
SaProt	LLR -7.84	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	Δ0.22	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 7.7	GERP 2.3, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 104 kb · p 0.09 · regional, not allelic
Overall
CADD	32.0	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: CC2D2A
Protein: p.Val975Asp
Coding: c.2924T>A
MANE Select: NM_001378615
dbSNP: rs1560183164
Type: single nucleotide variant
Location: chr4:15560532 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 69.46

Full CC2D2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CC2D2A p.Val975= Likely benign ★ same residue
CC2D2A c.1017+1G>A Pathogenic/Likely pathogenic ★★ same type
CC2D2A c.1149+1G>A Pathogenic/Likely pathogenic ★★ same type
CC2D2A c.123+2T>G Likely pathogenic ★★ same type
CC2D2A c.1359+1G>A Pathogenic/Likely pathogenic ★★ same type
CC2D2A c.1359+1G>C Likely pathogenic ★★ same type
CC2D2A c.1466+1G>A Likely pathogenic ★★ same type
CC2D2A c.1466+2T>C Likely pathogenic ★★ 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/cc2d2a-p-val975asp (accessed [today's date]).

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