Is CFAP52 p.Arg613Ter (c.1837C>T) pathogenic?

CFAP52 p.Arg613Ter (c.1837C>T) is classified Uncertain significance in CFAP52 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-05). Ultra-rare (popmax 0.0134%, eas).

How common is CFAP52 p.Arg613Ter (c.1837C>T) in the general population?

CFAP52 p.Arg613Ter (c.1837C>T) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

CFAP52 p.Arg613Ter

c.1837C>T · VCV4685187

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

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	escapes	premature termination codon in the last exon (14 of 14) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP -1.8, phastCons 1
Overall
CADD	37.0	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 0.0134% East Asian · 6/44,798 alleles

Filtering AF 0.0058% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00395%

Overall 0.00391% 63/1,611,384 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0134%	7,466
Admixed American	0.00672%	14,891
European (non-Finnish)	0.00433%	23,115
Remaining individualsnot grpmax-eligible	0.0016%	62,380
Finnishnot grpmax-eligible	0.00156%	64,006

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.Arg613Ter
Coding: c.1837C>T
MANE Select: NM_145054
Type: single nucleotide variant
Location: chr17:9643172 (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

Similar variants

CFAP52 p.Arg613Gln Uncertain significance ★ ⚠ same residue
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
CFAP52 p.Arg594Cys Uncertain significance ★★ ⚠ same type
CFAP52 p.Gly343Ser Uncertain significance ★★ ⚠ same type
CFAP52 p.Gly534Ala 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-arg613ter (accessed [today's date]).

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