Is CC2D1A p.Val628fs (c.1882_1891del) pathogenic?

CC2D1A p.Val628fs (c.18821891del) is classified Pathogenic in CC2D1A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-25). No gnomAD frequency available for this variant.

How common is CC2D1A p.Val628fs (c.1882_1891del) in the general population?

CC2D1A p.Val628fs (c.1882_1891del) is no gnomAD frequency available for this variant (gnomAD).

CC2D1A p.Val628fs

c.1882_1891del · rs2513119050 · VCV2705339

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 17 of 29
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5	GERP -0.16, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CC2D1A
Protein: p.Val628fs
Coding: c.1882_1891del
MANE Select: NM_017721
dbSNP: rs2513119050
Type: Deletion
Location: chr19:13923751 (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 c.511_513+1del Likely pathogenic ★★ same type
CC2D1A p.Gly898fs Pathogenic/Likely pathogenic ★★ same type
CC2D1A p.Lys116fs Pathogenic ★★ same type
CC2D1A c.1222+15_1222+29del Benign/Likely benign ★★ same type
CC2D1A c.2316+21del Likely benign ★★ same type
CC2D1A c.1940+2_1940+5del Likely pathogenic ★ same type
CC2D1A c.49_60+23del Likely pathogenic ★ same type
CC2D1A p.Glu379fs Likely pathogenic ★ 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-val628fs (accessed [today's date]).

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