RAD54L p.Phe73=
c.219T>C · rs2525660144 · VCV1787569
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000512%, nfe)
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 2.3 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 11.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000512%
European (non-Finnish) · 6/1,171,068 alleles
Filtering AF
0.000184%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000121%
Overall
0.000374%
6/1,604,446 alleles · very rare
exomes 6/1,452,058 · genomes 0/152,388 · joint denominator
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
- RAD54L
- Protein
- p.Phe73=
- Coding
- c.219T>C
- MANE Select
- NM_003579
- dbSNP
- rs2525660144
- Type
- single nucleotide variant
- Location
- chr1:46258694 (GRCh38)
- Gene constraint
- LOEUF 0.94 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.64 · 1 PDB
Similar variants
- RAD54L p.Arg542Cys Likely pathogenic ★★ same type
- RAD54L p.Cys295Arg Uncertain significance ★★ ⚠ same type
- RAD54L p.Gly94Ala Uncertain significance ★★ ⚠ same type
- RAD54L p.Met590Thr Uncertain significance ★★ ⚠ same type
- RAD54L p.Phe733Val Uncertain significance ★★ ⚠ same type
- RAD54L p.Pro483Arg Uncertain significance ★★ ⚠ same type
- RAD54L p.Ser443Thr Uncertain significance ★★ ⚠ same type
- RAD54L p.Ser520Leu 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/rad54l-p-phe73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown