Is CCDC8 p.Ser108fs (c.324_331del) pathogenic?

CCDC8 p.Ser108fs (c.324331del) is classified Likely pathogenic in CCDC8 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-29). Absent from gnomAD; Associated with 3M syndrome 3.

What condition is associated with CCDC8 p.Ser108fs (c.324_331del)?

CCDC8 p.Ser108fs (c.324_331del) is associated with 3M syndrome 3 (ClinVar).

How common is CCDC8 p.Ser108fs (c.324_331del) in the general population?

CCDC8 p.Ser108fs (c.324_331del) is absent from gnomAD (gnomAD).

CCDC8 p.Ser108fs

c.324_331del · rs2513602574 · VCV3065843

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

Conditions

3M syndrome 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (1 of 1) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.5	GERP 1.4, 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: CCDC8
Protein: p.Ser108fs
Coding: c.324_331del
MANE Select: NM_032040
dbSNP: rs2513602574
Type: Deletion
Location: chr19:46412480 (GRCh38)
Gene constraint: LOEUF 1.796 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 46.83 · 1 PDB
Residue 108: the 'disordered' region

Full CCDC8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

3M syndrome 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CCDC8 p.Gln327fs Pathogenic/Likely pathogenic ★★ same condition
CCDC8 p.Glu337_Arg344del Uncertain significance ★★ same condition
CCDC8 p.Ala323fs Likely pathogenic ★ same condition
CCDC8 p.Ala353fs Likely pathogenic ★ same condition
CCDC8 p.Asp247fs Likely pathogenic ★ same condition
CCDC8 p.Gln68fs Likely pathogenic ★ same condition
CCDC8 p.Gly95fs Likely pathogenic ★ same condition
CCDC8 p.Asn270fs 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/ccdc8-p-ser108fs (accessed [today's date]).

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