Is CEP41 p.Asp55fs (c.162del) pathogenic?

CEP41 p.Asp55fs (c.162del) is classified Pathogenic in CEP41 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-26). Very rare (popmax 0.000895%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CEP41 p.Asp55fs (c.162del)?

CEP41 p.Asp55fs (c.162del) is associated with Inborn genetic diseases (ClinVar).

How common is CEP41 p.Asp55fs (c.162del) in the general population?

CEP41 p.Asp55fs (c.162del) is very rare (popmax 0.000895%, nfe) (gnomAD).

CEP41 p.Asp55fs

c.162del · VCV4839576

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000895%, nfe)

Conditions

Inborn genetic diseases

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 4 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.3, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000895% European (non-Finnish) · 10/1,117,362 alleles

Filtering AF 0.000453% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00033%

Overall 0.000718% 10/1,392,718 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: CEP41
Protein: p.Asp55fs
Coding: c.162del
MANE Select: NM_018718
Type: Deletion
Location: chr7:130412224 (GRCh38)
Gene constraint: LOEUF 1.066 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.06 · 1 PDB

Full CEP41 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEP41 p.Asp55Val Uncertain significance ★ ⚠ same residue
CEP41 p.Asp55= Likely benign ★ same residue
CEP41 p.Arg286Ter Pathogenic/Likely pathogenic ★★ same condition
CEP41 p.Ala258Val Uncertain significance ★★ ⚠ same condition
CEP41 p.Ala354Val Uncertain significance ★★ ⚠ same condition
CEP41 p.Arg326Leu Uncertain significance ★★ ⚠ same condition
CEP41 p.Asn347Ser Uncertain significance ★★ ⚠ same condition
CEP41 p.Gln185Glu Uncertain significance ★★ ⚠ 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/cep41-p-asp55fs (accessed [today's date]).

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