Is CCDC88C p.Lys115fs (c.343_367del) pathogenic?

CCDC88C p.Lys115fs (c.343367del) is classified Pathogenic in CCDC88C (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-06). Absent from gnomAD.

How common is CCDC88C p.Lys115fs (c.343_367del) in the general population?

CCDC88C p.Lys115fs (c.343_367del) is absent from gnomAD (gnomAD).

CCDC88C p.Lys115fs

c.343_367del · rs2544478310 · VCV2852172

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 5 of 30
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.1	GERP 1, phastCons 1
Region caveats
Repeat context	tandem	(CAGCAC)n simple repeat · ambiguous alignment · confidence, not pathogenicity

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: CCDC88C
Protein: p.Lys115fs
Coding: c.343_367del
MANE Select: NM_001080414
dbSNP: rs2544478310
Type: Deletion
Location: chr14:91343631 (GRCh38)
Gene constraint: LOEUF 0.759 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.69
Residue 115: the calponin-homology (ch) domain

Full CCDC88C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC88C p.His1792_Ala1793del Uncertain significance ★★ same type
CCDC88C c.4113-1_4117del Likely pathogenic ★ same type
CCDC88C c.4583_4630+11del Likely pathogenic ★ same type
CCDC88C p.Ala364fs Pathogenic ★ same type
CCDC88C p.Ala883fs Pathogenic ★ same type
CCDC88C p.Asp2fs Pathogenic ★ same type
CCDC88C p.Gln829fs Pathogenic ★ same type
CCDC88C p.Glu1149fs 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/ccdc88c-p-lys115fs (accessed [today's date]).

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