Is CEP78 p.Val71fs (c.211del) pathogenic?

CEP78 p.Val71fs (c.211del) is classified Likely pathogenic in CEP78 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-20). Very rare (popmax 8.58e-05%, nfe); Associated with CEP78-related disorder.

What condition is associated with CEP78 p.Val71fs (c.211del)?

CEP78 p.Val71fs (c.211del) is associated with CEP78-related disorder (ClinVar).

How common is CEP78 p.Val71fs (c.211del) in the general population?

CEP78 p.Val71fs (c.211del) is very rare (popmax 8.58e-05%, nfe) (gnomAD).

CEP78 p.Val71fs

c.211del · rs1363491382 · VCV867155

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 8.58e-05%, nfe)

Conditions

CEP78-related disorder

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 1 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.1	GERP -2.7, phastCons 0.044
Overall
CADD	23.6	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.58e-05% European (non-Finnish) · 1/1,165,528 alleles

Overall 0.000126% 2/1,585,176 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00164%	60,952
European (non-Finnish)grpmax	8.58e-05%	1,165,528

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CEP78
Protein: p.Val71fs
Coding: c.211del
MANE Select: NM_001330691
dbSNP: rs1363491382
Type: Deletion
Location: chr9:78236560 (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

Disease context

CEP78-related disorder

Similar variants

CEP78 p.Glu472fs Pathogenic/Likely pathogenic ★★ same condition
CEP78 p.Lys179fs Pathogenic ★★ same condition
CEP78 p.Ser485fs Pathogenic/Likely pathogenic ★★ same condition
CEP78 p.Trp212fs Pathogenic ★★ same condition
CEP78 p.Asp67fs Likely pathogenic ★ same condition
CEP78 p.Gly241fs Likely pathogenic ★ same condition
CEP78 p.Gly420fs Likely pathogenic ★ same condition
CEP78 p.Phe15fs 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/cep78-p-val71fs (accessed [today's date]).

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