Is CFAP52 p.Arg183Ter (c.547C>T) pathogenic?

CFAP52 p.Arg183Ter (c.547C>T) is classified Likely pathogenic in CFAP52 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-26). Very rare (popmax 0.00224%, eas); Associated with heterotaxy, visceral, 10, autosomal, with male infertility.

What condition is associated with CFAP52 p.Arg183Ter (c.547C>T)?

CFAP52 p.Arg183Ter (c.547C>T) is associated with heterotaxy, visceral, 10, autosomal, with male infertility (ClinVar).

How common is CFAP52 p.Arg183Ter (c.547C>T) in the general population?

CFAP52 p.Arg183Ter (c.547C>T) is very rare (popmax 0.00224%, eas) (gnomAD).

CFAP52 p.Arg183Ter

c.547C>T · rs775639416 · VCV3065385

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00224%, eas)

Conditions

heterotaxy, visceral, 10, autosomal, with male infertility

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 5 of 14
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.29	loss · gain 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 4.8	GERP 1.5, phastCons 1
Overall
CADD	42.0	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 0.00224% East Asian · 1/44,586 alleles

Filtering AF 0.000125% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.1e-05%

Overall 0.000436% 7/1,605,228 alleles · very rare exomes 7/1,455,232 · genomes 0/149,996 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00224%	44,586
Finnishnot grpmax-eligible	0.00162%	61,862
European (non-Finnish)	0.000425%	235,318

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: CFAP52
Protein: p.Arg183Ter
Coding: c.547C>T
MANE Select: NM_145054
dbSNP: rs775639416
Type: single nucleotide variant
Location: chr17:9598244 (GRCh38)
Gene constraint: LOEUF 1.022 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.59 · 2 PDB

Full CFAP52 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

heterotaxy, visceral, 10, autosomal, with male infertility — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CFAP52 p.Arg407Ter Likely pathogenic ★ same condition
CFAP52 p.Gly271Arg Uncertain significance ★ ⚠ same condition
CFAP52 c.71-1591_270+1del Uncertain significance ★ same condition
CFAP52 p.Gly435fs Conflicting classifications of pathogenicity ★ same condition
CFAP52 p.Ala147Thr Uncertain significance ★★ ⚠ same type
CFAP52 p.Ala161Asp Uncertain significance ★★ ⚠ same type
CFAP52 p.Arg106Gln Uncertain significance ★★ ⚠ same type
CFAP52 p.Arg170Gln 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/cfap52-p-arg183ter (accessed [today's date]).

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