Is CC2D1A p.Asp854= (c.2562C>T) pathogenic?

CC2D1A p.Asp854= (c.2562C>T) is classified Likely benign in CC2D1A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-11). Very rare (popmax 0.005%, amr).

How common is CC2D1A p.Asp854= (c.2562C>T) in the general population?

CC2D1A p.Asp854= (c.2562C>T) is very rare (popmax 0.005%, amr) (gnomAD).

CC2D1A p.Asp854=

c.2562C>T · VCV3692957

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

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 1.2	GERP -3.9, phastCons 1
Overall
CADD	8.072	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/59,968 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000186% 3/1,613,488 alleles · very rare exomes 3/1,461,498 · genomes 0/151,990 · joint denominator

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.Asp854=
Coding: c.2562C>T
MANE Select: NM_017721
Type: single nucleotide variant
Location: chr19:13929421 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.71 · 1 PDB

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

Similar variants

CC2D1A p.Asp854Glu Uncertain significance ★ ⚠ 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
CC2D1A c.2073+5G>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-asp854 (accessed [today's date]).

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