Is CEP152 p.Arg250fs (c.749_750del) pathogenic?

CEP152 p.Arg250fs (c.749750del) is classified Pathogenic in CEP152 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-16). Very rare (popmax 0.00017%, nfe).

How common is CEP152 p.Arg250fs (c.749_750del) in the general population?

CEP152 p.Arg250fs (c.749_750del) is very rare (popmax 0.00017%, nfe) (gnomAD).

CEP152 p.Arg250fs

c.749_750del · rs1897109421 · VCV2999378

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00017%, nfe)

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 7 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 5.4, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00017% European (non-Finnish) · 2/1,179,860 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000137% 2/1,461,552 alleles · very rare

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: CEP152
Protein: p.Arg250fs
Coding: c.749_750del
MANE Select: NM_001194998
dbSNP: rs1897109421
Type: Microsatellite
Location: chr15:48793403 (GRCh38)
Gene constraint: LOEUF 0.784 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.54 · 3 PDB

Full CEP152 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP152 p.Glu301fs Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Lys586del Uncertain significance ★★ same type
CEP152 p.Glu27fs Pathogenic ★ same type
CEP152 p.Leu483fs Pathogenic ★ same type
CEP152 p.Ser232fs Pathogenic ★ same type
CEP152 p.Ser47fs Likely pathogenic ★ same type
CEP152 p.Cys1407fs Uncertain significance ★ same type
CEP152 p.Gln224del Uncertain significance ★ 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/cep152-p-arg250fs (accessed [today's date]).

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