Is CC2D1A p.Asp656Val (c.1967A>T) pathogenic?

CC2D1A p.Asp656Val (c.1967A>T) is classified Uncertain significance in CC2D1A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-05). AlphaMissense: ambiguous (0.3707); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CC2D1A p.Asp656Val (c.1967A>T)?

CC2D1A p.Asp656Val (c.1967A>T) is associated with Inborn genetic diseases (ClinVar).

How common is CC2D1A p.Asp656Val (c.1967A>T) in the general population?

CC2D1A p.Asp656Val (c.1967A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CC2D1A p.Asp656Val (c.1967A>T)?

AlphaMissense predicts ambiguous (score 0.3707) — an in-silico prediction, not a clinical call.

CC2D1A p.Asp656Val

c.1967A>T · VCV3827977

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3707 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3707	ambiguous
REVEL	0.537	indeterminate
SaProt	LLR -10.12	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.4, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 24 kb · p 0.0034 · regional, not allelic
Overall
CADD	25.0	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: CC2D1A
Protein: p.Asp656Val
Coding: c.1967A>T
MANE Select: NM_017721
Type: single nucleotide variant
Location: chr19:13926543 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.71 · 1 PDB
Residue 656: the c2 domain

Full CC2D1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CC2D1A p.Asp656Asn Uncertain significance ★★ ⚠ same residue
CC2D1A c.61-2A>G Likely pathogenic ★★ same condition
CC2D1A c.1941-6C>T Uncertain significance ★★ same condition
CC2D1A c.2073+5G>T Uncertain significance ★★ same condition
CC2D1A c.946+6A>G Uncertain significance ★★ same condition
CC2D1A p.Ala154Thr Uncertain significance ★★ ⚠ same condition
CC2D1A p.Ala481Val Uncertain significance ★★ ⚠ same condition
CC2D1A p.Ala507Val Uncertain significance ★★ ⚠ same condition

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/cc2d1a-p-asp656val (accessed [today's date]).

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