CFAP53 p.Gln31=
c.93A>G · rs3744849 · VCV2648717
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.221%, eas)
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 -1.1 | GERP 0.61 |
| Overall | ||
| CADD | 2.491 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.221%
East Asian · 99/44,888 alleles
Filtering AF
0.185%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.172%
Overall
0.00818%
132/1,614,106 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.221% | 453 |
| South Asian | 0.0143% | 7,006 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,929 |
| Admixed American | 0.00333% | 30,009 |
| European (non-Finnish) | 0.000932% | 107,268 |
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.Gln31=
- Coding
- c.93A>G
- MANE Select
- NM_145020
- dbSNP
- rs3744849
- Type
- single nucleotide variant
- Location
- chr18:50262196 (GRCh38)
- Gene constraint
- LOEUF 1.282 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.17 · 2 PDB
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-gln31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown