CFAP45 p.Arg390=
c.1168C>A · VCV3341788
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
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 1.8 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 9.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,080 alleles
Filtering AF
0.000688%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.00116%
17/1,461,864 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,540 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| European (non-Finnish) | 0.00119% | 84,287 |
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
- CFAP45
- Protein
- p.Arg390=
- Coding
- c.1168C>A
- MANE Select
- NM_012337
- Type
- single nucleotide variant
- Location
- chr1:159876740 (GRCh38)
- Gene constraint
- LOEUF 0.713 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.03 · 2 PDB
- Residue 390
- the trichohyalin-plectin-homology domain; a UniProt-annotated variant site (in htx11; loss of panaxonemal expression in respiratory cilia and in sperm flagella)
Similar variants
- CFAP45 p.Arg390Trp Uncertain significance ★ ⚠ same residue
- CFAP45 p.Asp320Tyr Uncertain significance ★★ ⚠ same type
- CFAP45 p.Lys518Glu Uncertain significance ★★ ⚠ same type
- CFAP45 p.Asp222Gly Benign ★★ ⚠ same type
- CFAP45 p.Arg350Ter Likely pathogenic ★ same type
- CFAP45 p.Ala15Pro Uncertain significance ★ ⚠ same type
- CFAP45 p.Ala370Pro Uncertain significance ★ ⚠ same type
- CFAP45 p.Ala436Val 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/cfap45-p-arg390 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown