Is CFAP53 p.Leu292= (c.876A>T) pathogenic?

CFAP53 p.Leu292= (c.876A>T) is classified Likely benign in CFAP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-12). Very rare (popmax 0.00266%, afr).

How common is CFAP53 p.Leu292= (c.876A>T) in the general population?

CFAP53 p.Leu292= (c.876A>T) is very rare (popmax 0.00266%, afr) (gnomAD).

CFAP53 p.Leu292=

c.876A>T · rs748351880 · VCV718963

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00266%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.46	GERP -3.5, phastCons 0.99
Overall
CADD	0.531	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00266% African / African-American · 2/75,068 alleles

Filtering AF 0.000542% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000428%

Overall 0.00103% 15/1,461,852 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00266%	37,534
Remaining individualsnot grpmax-eligible	0.0016%	62,508
European (non-Finnish)	0.00102%	98,335

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: CFAP53
Protein: p.Leu292=
Coding: c.876A>T
MANE Select: NM_145020
dbSNP: rs748351880
Type: single nucleotide variant
Location: chr18:50250878 (GRCh38)
Gene constraint: LOEUF 1.282 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.17 · 2 PDB
Residue 292: the trichohyalin-plectin-homology domain; a UniProt-annotated variant site (in htx6; uncertain significance; no overt effects on the structure or function of respiratory cilia)

Full CFAP53 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP53 p.Ala185Thr Uncertain significance ★★ ⚠ same type
CFAP53 p.Ala385Ser Uncertain significance ★★ ⚠ same type
CFAP53 p.Arg158Gly Uncertain significance ★★ ⚠ same type
CFAP53 p.Arg257Cys Uncertain significance ★★ ⚠ same type
CFAP53 p.Arg470His Uncertain significance ★★ ⚠ same type
CFAP53 p.Arg505His Uncertain significance ★★ ⚠ same type
CFAP53 p.Arg505Leu Uncertain significance ★★ ⚠ same type
CFAP53 p.Arg505Ser 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/cfap53-p-leu292 (accessed [today's date]).

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