Is CC2D1A p.Lys696= (c.2088A>G) pathogenic?

CC2D1A p.Lys696= (c.2088A>G) is classified Benign/Likely benign in CC2D1A (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-09). Rare (popmax 0.856%, afr); Associated with Inborn genetic diseases.

What condition is associated with CC2D1A p.Lys696= (c.2088A>G)?

CC2D1A p.Lys696= (c.2088A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CC2D1A p.Lys696= (c.2088A>G) in the general population?

CC2D1A p.Lys696= (c.2088A>G) is rare (popmax 0.856%, afr) (gnomAD).

CC2D1A p.Lys696=

c.2088A>G · rs73925404 · VCV434607

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.856%, afr)

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 1.2	GERP -1.6, phastCons 1
Overall
CADD	8.22	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.856% African / African-American · 642/75,014 alleles

Filtering AF 0.801% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.779%

Overall 0.0457% 737/1,614,064 alleles · rare exomes 338/1,461,870 · genomes 399/152,194 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.856%	117
Admixed American	0.0717%	1,395
Remaining individualsnot grpmax-eligible	0.048%	2,084
Middle Eastern	0.0165%	6,062
European (non-Finnish)	0.00169%	59,000
South Asian	0.0011%	91,080

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.Lys696=
Coding: c.2088A>G
MANE Select: NM_017721
dbSNP: rs73925404
Type: single nucleotide variant
Location: chr19:13926835 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.71 · 1 PDB
Residue 696: 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 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-lys696 (accessed [today's date]).

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