Is CEP78 p.Pro430fs (c.1285_1288dup) pathogenic?

CEP78 p.Pro430fs (c.12851288dup) is classified Pathogenic in CEP78 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-27). Absent from gnomAD.

How common is CEP78 p.Pro430fs (c.1285_1288dup) in the general population?

CEP78 p.Pro430fs (c.1285_1288dup) is absent from gnomAD (gnomAD).

CEP78 p.Pro430fs

c.1285_1288dup · rs2489471559 · VCV2737535

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 11 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.3	GERP 0.56, 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: CEP78
Protein: p.Pro430fs
Coding: c.1285_1288dup
MANE Select: NM_001330691
dbSNP: rs2489471559
Type: Duplication
Location: chr9:78254868 (GRCh38)
Gene constraint: LOEUF 1.531 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.28

Full CEP78 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP78 p.Leu127fs Pathogenic/Likely pathogenic ★★ same type
CEP78 c.1380+18dup Benign/Likely benign ★★ same type
CEP78 c.1626-6dup Benign/Likely benign ★★ same type
CEP78 p.Arg314fs Pathogenic ★ same type
CEP78 p.Arg95fs Pathogenic ★ same type
CEP78 p.Gln469fs Pathogenic ★ same type
CEP78 p.Gln564fs Likely pathogenic ★ same type
CEP78 p.Glu576fs 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/cep78-p-pro430fs (accessed [today's date]).

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