Is CEP250 p.Arg147fs (c.439del) pathogenic?

CEP250 p.Arg147fs (c.439del) is classified Pathogenic in CEP250 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-18). Absent from gnomAD.

How common is CEP250 p.Arg147fs (c.439del) in the general population?

CEP250 p.Arg147fs (c.439del) is absent from gnomAD (gnomAD).

CEP250 p.Arg147fs

c.439del · rs2515583042 · VCV2733217

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 7 of 35
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8.7	GERP -2.4, 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: CEP250
Protein: p.Arg147fs
Coding: c.439del
MANE Select: NM_007186
dbSNP: rs2515583042
Type: Deletion
Location: chr20:35466150 (GRCh38)
Gene constraint: LOEUF 0.86 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.68 · 1 PDB
Residue 147: a UniProt-annotated variant site (in crdhl2)

Full CEP250 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP250 p.Arg147Gln Uncertain significance ★ ⚠ same residue
CEP250 p.Arg147Trp Uncertain significance ★ ⚠ same residue
CEP250 p.Asp1684fs Pathogenic ★★ same type
CEP250 p.Glu883fs Pathogenic/Likely pathogenic ★★ same type
CEP250 p.Met885fs Pathogenic/Likely pathogenic ★★ same type
CEP250 p.Glu1735del Uncertain significance ★★ same type
CEP250 p.Glu2151_Arg2154del Uncertain significance ★★ same type
CEP250 p.Lys1664del 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/cep250-p-arg147fs (accessed [today's date]).

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