Is CCDC68 p.Ser259fs (c.775dup) pathogenic?

CCDC68 p.Ser259fs (c.775dup) is classified Likely pathogenic in CCDC68 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-01-27). Absent from gnomAD; Associated with Recurrent spontaneous abortion.

What condition is associated with CCDC68 p.Ser259fs (c.775dup)?

CCDC68 p.Ser259fs (c.775dup) is associated with Recurrent spontaneous abortion (ClinVar).

How common is CCDC68 p.Ser259fs (c.775dup) in the general population?

CCDC68 p.Ser259fs (c.775dup) is absent from gnomAD (gnomAD).

CCDC68 p.Ser259fs

c.775dup · rs2044011378 · VCV812695

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Recurrent spontaneous abortion

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 9 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.24	GERP -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: CCDC68
Protein: p.Ser259fs
Coding: c.775dup
MANE Select: NM_025214
dbSNP: rs2044011378
Type: Duplication
Location: chr18:54919284 (GRCh38)
Gene constraint: LOEUF 0.923 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 81.20

Full CCDC68 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Recurrent spontaneous abortion — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CCDC68 p.Ser259Arg Uncertain significance ★ ⚠ same residue

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/ccdc68-p-ser259fs (accessed [today's date]).

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