Is CC2D1A p.Ala479= (c.1437C>T) pathogenic?

CC2D1A p.Ala479= (c.1437C>T) is classified Uncertain significance in CC2D1A (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-10). Absent from gnomAD v4.1; Associated with intellectual disability, autosomal recessive 3.

What condition is associated with CC2D1A p.Ala479= (c.1437C>T)?

CC2D1A p.Ala479= (c.1437C>T) is associated with intellectual disability, autosomal recessive 3 (ClinVar).

How common is CC2D1A p.Ala479= (c.1437C>T) in the general population?

CC2D1A p.Ala479= (c.1437C>T) is absent from gnomAD v4.1 (gnomAD).

CC2D1A p.Ala479=

c.1437C>T · rs1971378002 · VCV1033856

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

intellectual disability, autosomal recessive 3

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 1.1	GERP -0.08, phastCons 1
Overall
CADD	9.571	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CC2D1A
Protein: p.Ala479=
Coding: c.1437C>T
MANE Select: NM_017721
dbSNP: rs1971378002
Type: single nucleotide variant
Location: chr19:13920637 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.71 · 1 PDB
Residue 479: the 'disordered' region

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

Disease context

intellectual disability, autosomal recessive 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CC2D1A c.2225+1G>A Likely pathogenic ★★ same condition
CC2D1A c.2454+1G>A Likely pathogenic ★★ same condition
CC2D1A c.2710+1G>A Likely pathogenic ★★ same condition
CC2D1A c.61-2A>G Likely pathogenic ★★ same condition
CC2D1A c.748+1G>T Pathogenic ★★ same condition
CC2D1A c.2073+5G>T Uncertain significance ★★ same condition
CC2D1A p.Ala154Thr Uncertain significance ★★ ⚠ same condition
CC2D1A p.Ala481Val 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-ala479 (accessed [today's date]).

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