Is CC2D2A p.Arg1049Pro (c.3146G>C) pathogenic?

CC2D2A p.Arg1049Pro (c.3146G>C) is classified Uncertain significance in CC2D2A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-13). AlphaMissense: likely pathogenic (0.9909); Absent from gnomAD v4.1.

How common is CC2D2A p.Arg1049Pro (c.3146G>C) in the general population?

CC2D2A p.Arg1049Pro (c.3146G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CC2D2A p.Arg1049Pro (c.3146G>C)?

AlphaMissense predicts likely pathogenic (score 0.9909) — an in-silico prediction, not a clinical call.

CC2D2A p.Arg1049Pro

c.3146G>C · VCV4057104

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9909 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9909	likely pathogenic · top 1% in CC2D2A
REVEL	0.718	pathogenic-leaning
SaProt	LLR -12.49	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 2.7, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 104 kb · p 0.09 · regional, not allelic
Overall
CADD	27.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

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.Arg1049Pro
Coding: c.3146G>C
MANE Select: NM_001378615
Type: single nucleotide variant
Location: chr4:15563486 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 69.46
Residue 1049: the c2 domain

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

Similar variants

CC2D2A p.Arg1049Ter Pathogenic ★★ same residue
CC2D2A p.Arg1049Gln Uncertain significance ★★ ⚠ same residue
CC2D2A p.Arg1049= Likely benign ★ same residue
CC2D2A p.Arg1049Gly Likely pathogenic ⚠ 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

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-arg1049pro (accessed [today's date]).

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