Is CC2D2A p.Pro815fs (c.2444del) pathogenic?

CC2D2A p.Pro815fs (c.2444del) is classified Likely pathogenic in CC2D2A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-15). Associated with Meckel syndrome, type 6.

What condition is associated with CC2D2A p.Pro815fs (c.2444del)?

CC2D2A p.Pro815fs (c.2444del) is associated with Meckel syndrome, type 6, Joubert syndrome 9, retinitis pigmentosa 93 (ClinVar).

CC2D2A p.Pro815fs

c.2444del · VCV3590369

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Meckel syndrome, type 6

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 19 of 37
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.8	GERP -5.2

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

Variant & gene context

Gene: CC2D2A
Protein: p.Pro815fs
Coding: c.2444del
MANE Select: NM_001378615
Type: Deletion
Location: chr4:15553262 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 69.46

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

Disease context

Meckel syndrome, type 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Joubert syndrome 9 retinitis pigmentosa 93 COACH syndrome 2

Similar variants

CC2D2A c.3289delG Pathogenic ★★ same condition
CC2D2A c.3597_3600del Pathogenic/Likely pathogenic ★★ same condition
CC2D2A c.4179+1del Pathogenic ★★ same condition
CC2D2A p.Ala1197fs Pathogenic/Likely pathogenic ★★ same condition
CC2D2A p.Ala447fs Pathogenic/Likely pathogenic ★★ same condition
CC2D2A p.Asp1227fs Likely pathogenic ★★ same condition
CC2D2A p.Asp1489fs Pathogenic/Likely pathogenic ★★ same condition
CC2D2A p.Gln280fs Pathogenic/Likely pathogenic ★★ 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/cc2d2a-p-pro815fs (accessed [today's date]).

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