Is CC2D1A p.Ala397= (c.1191C>G) pathogenic?

CC2D1A p.Ala397= (c.1191C>G) is classified Likely benign in CC2D1A (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-12-18). Ultra-rare (popmax 0.015%, amr); Associated with Inborn genetic diseases.

What condition is associated with CC2D1A p.Ala397= (c.1191C>G)?

CC2D1A p.Ala397= (c.1191C>G) is associated with Inborn genetic diseases (ClinVar).

How common is CC2D1A p.Ala397= (c.1191C>G) in the general population?

CC2D1A p.Ala397= (c.1191C>G) is ultra-rare (popmax 0.015%, amr) (gnomAD).

CC2D1A p.Ala397=

c.1191C>G · rs749937867 · VCV1744932

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.015%, amr)

Conditions

Inborn genetic diseases

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 -9.7	GERP -4.8
Overall
CADD	0.25	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.015% Admixed American · 9/59,964 alleles

Filtering AF 0.00774% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00579%

Overall 0.000682% 11/1,612,890 alleles · ultra-rare exomes 10/1,460,738 · genomes 1/152,152 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.015%	6,663
East Asian	0.00223%	44,866
Remaining individualsnot grpmax-eligible	0.0016%	62,430

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.Ala397=
Coding: c.1191C>G
MANE Select: NM_017721
dbSNP: rs749937867
Type: single nucleotide variant
Location: chr19:13919171 (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

Disease context

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

Similar variants

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
CC2D1A p.Ala50Ser 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-ala397 (accessed [today's date]).

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