Is CC2D1A p.Pro330= (c.990G>A) pathogenic?

CC2D1A p.Pro330= (c.990G>A) is classified Likely benign in CC2D1A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-19). Ultra-rare (popmax 0.0989%, sas); Associated with Inborn genetic diseases.

What condition is associated with CC2D1A p.Pro330= (c.990G>A)?

CC2D1A p.Pro330= (c.990G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CC2D1A p.Pro330= (c.990G>A) in the general population?

CC2D1A p.Pro330= (c.990G>A) is ultra-rare (popmax 0.0989%, sas) (gnomAD).

CC2D1A p.Pro330=

c.990G>A · rs202106696 · VCV1768577

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0989%, sas)

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 -3.8	GERP -4.5
Overall
CADD	0.532	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0989% South Asian · 90/90,966 alleles

Filtering AF 0.0824% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0762%

Overall 0.0164% 265/1,613,294 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0989%	1,011
Admixed American	0.0284%	3,526
Middle Eastern	0.0165%	6,050
Remaining individualsnot grpmax-eligible	0.0128%	7,810
European (non-Finnish)	0.0125%	8,025
East Asian	0.00446%	22,428

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.Pro330=
Coding: c.990G>A
MANE Select: NM_017721
dbSNP: rs202106696
Type: single nucleotide variant
Location: chr19:13918789 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.71 · 1 PDB
Residue 330: the 'disordered' region

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 p.Pro330Arg Uncertain significance ★ ⚠ same residue
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

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-pro330 (accessed [today's date]).

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