Is CFAP61 p.Ile151fs (c.452_453del) pathogenic?

CFAP61 p.Ile151fs (c.452453del) is classified Pathogenic in CFAP61 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-06-02). Very rare (popmax 0.0011%, sas); Associated with spermatogenic failure 84.

What condition is associated with CFAP61 p.Ile151fs (c.452_453del)?

CFAP61 p.Ile151fs (c.452_453del) is associated with spermatogenic failure 84 (ClinVar).

How common is CFAP61 p.Ile151fs (c.452_453del) in the general population?

CFAP61 p.Ile151fs (c.452_453del) is very rare (popmax 0.0011%, sas) (gnomAD).

CFAP61 p.Ile151fs

c.452_453del · rs2515805050 · VCV2504101

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

spermatogenic failure 84

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 6 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.88	GERP -2.1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,074 alleles

Overall 6.84e-05% 1/1,461,754 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: CFAP61
Protein: p.Ile151fs
Coding: c.452_453del
MANE Select: NM_015585
dbSNP: rs2515805050
Type: Deletion
Location: chr20:20075500 (GRCh38)
Gene constraint: LOEUF 0.892 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.86 · 1 PDB

Full CFAP61 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spermatogenic failure 84 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CFAP61 p.Ile151Leu Uncertain significance ★ ⚠ same residue
CFAP61 p.Arg552Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
CFAP61 c.3125-1G>C Likely pathogenic ★ same condition
CFAP61 p.Arg283Ter Pathogenic ★ same condition
CFAP61 c.143+5G>A Pathogenic same condition
CFAP61 c.144-2A>G Pathogenic same condition
CFAP61 p.Asp971Asn Pathogenic ⚠ same condition
CFAP61 p.Gly556Arg 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/cfap61-p-ile151fs (accessed [today's date]).

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