Is CC2D2A p.Asp21fs (c.62delinsTC) pathogenic?

CC2D2A p.Asp21fs (c.62delinsTC) is classified Likely pathogenic in CC2D2A (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-10). Absent from gnomAD.

How common is CC2D2A p.Asp21fs (c.62delinsTC) in the general population?

CC2D2A p.Asp21fs (c.62delinsTC) is absent from gnomAD (gnomAD).

CC2D2A p.Asp21fs

c.62delinsTC · rs1577309042 · VCV817142

Likely pathogenic Single submitter

Classification

Likely 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 3 of 37
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.5	GERP 0.92, 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: CC2D2A
Protein: p.Asp21fs
Coding: c.62delinsTC
MANE Select: NM_001378615
dbSNP: rs1577309042
Type: Indel
Location: chr4:15478745 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 69.46
Residue 21: the 'disordered' region

Full CC2D2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CC2D2A p.Asp21= Likely benign ★ same residue
CC2D2A p.Thr1297Arg Uncertain significance ★★ same type
CC2D2A p.Leu314fs Pathogenic ★ same type
CC2D2A p.Ser133fs Likely pathogenic ★ same type
CC2D2A c.2182-9_2182-8delinsAA Conflicting classifications of pathogenicity ★ same type
CC2D2A p.Leu1014Gly Uncertain significance ★ same type
CC2D2A p.Lys1382Ala Uncertain significance ★ same type
CC2D2A p.Pro1066_Ser1067= Uncertain significance ★ 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/cc2d2a-p-asp21fs (accessed [today's date]).

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