Is CC2D1A p.Arg265= (c.795C>T) pathogenic?

CC2D1A p.Arg265= (c.795C>T) is classified Likely benign in CC2D1A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-20). Ultra-rare (popmax 0.0959%, mid).

How common is CC2D1A p.Arg265= (c.795C>T) in the general population?

CC2D1A p.Arg265= (c.795C>T) is ultra-rare (popmax 0.0959%, mid) (gnomAD).

CC2D1A p.Arg265=

c.795C>T · rs373905397 · VCV2912533

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0959%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -20	GERP -4.7
Overall
CADD	0.017	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0959% Middle Eastern · 5/5,212 alleles

Filtering AF 0.0377% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0245%

Overall 0.00285% 46/1,612,264 alleles · ultra-rare exomes 37/1,460,014 · genomes 9/152,250 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0959%	1,042
South Asian	0.00989%	10,107
African / African-American	0.00668%	14,979
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,592
European (non-Finnish)	0.00212%	47,192
Admixed American	0.00167%	59,926

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: CC2D1A
Protein: p.Arg265=
Coding: c.795C>T
MANE Select: NM_017721
dbSNP: rs373905397
Type: single nucleotide variant
Location: chr19:13918116 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.71 · 1 PDB
Residue 265: the 'disordered' region

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

Similar variants

CC2D1A p.Arg265His Conflicting classifications of pathogenicity ★ ⚠ same residue
CC2D1A p.Arg265Cys Likely benign ★ ⚠ same residue
CC2D1A c.2225+1G>A Likely pathogenic ★★ same type
CC2D1A c.2454+1G>A Likely pathogenic ★★ same type
CC2D1A c.2710+1G>A Likely pathogenic ★★ same type
CC2D1A c.61-2A>G Likely pathogenic ★★ same type
CC2D1A c.748+1G>T Pathogenic ★★ same type
CC2D1A c.1941-6C>T 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/cc2d1a-p-arg265 (accessed [today's date]).

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