Is CEP152 p.Ser600fs (c.1797del) pathogenic?

CEP152 p.Ser600fs (c.1797del) is classified Pathogenic in CEP152 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-26). Very rare (popmax 0.0017%, nfe).

How common is CEP152 p.Ser600fs (c.1797del) in the general population?

CEP152 p.Ser600fs (c.1797del) is very rare (popmax 0.0017%, nfe) (gnomAD).

CEP152 p.Ser600fs

c.1797del · rs531410403 · VCV2990413

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0017%, 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 14 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP 4.4, phastCons 0.2
Overall
CADD	22.0	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 0.0017% European (non-Finnish) · 20/1,174,334 alleles

Filtering AF 0.00111% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000904%

Overall 0.00124% 20/1,606,850 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.Ser600fs
Coding: c.1797del
MANE Select: NM_001194998
dbSNP: rs531410403
Type: Deletion
Location: chr15:48769067 (GRCh38)
Gene constraint: LOEUF 0.784 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.54 · 3 PDB
Residue 600: the 'disordered' region

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

Similar variants

CEP152 p.Gln1058fs Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Leu1071fs Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Lys764fs Likely pathogenic ★★ same type
CEP152 p.Phe225_Leu226insTer Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Thr1006fs Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Thr386fs Pathogenic ★★ same type
CEP152 p.Tyr678_Gln679delinsTer Pathogenic ★★ same type
CEP152 p.Val1084fs Pathogenic/Likely 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/cep152-p-ser600fs (accessed [today's date]).

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