RHBDF2 p.Phe265=
c.795T>C · rs557022830 · VCV2892443
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0714%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.21 | gain · loss 0.16 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP -0.72, phastCons 1 |
| Overall | ||
| CADD | 11.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0714%
South Asian · 65/91,072 alleles
Filtering AF
0.0574%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0524%
Overall
0.00787%
127/1,613,770 alleles · ultra-rare
exomes 117/1,461,576 · genomes 10/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0714% | 1,401 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0574% | 1,741 |
| Admixed American | 0.0433% | 2,308 |
| Middle Eastern | 0.0165% | 6,056 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| Finnishnot grpmax-eligible | 0.00156% | 63,974 |
| African / African-American | 0.00133% | 75,008 |
| European (non-Finnish) | 0.000763% | 131,089 |
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
- RHBDF2
- Protein
- p.Phe265=
- Coding
- c.795T>C
- MANE Select
- NM_001005498
- dbSNP
- rs557022830
- Type
- single nucleotide variant
- Location
- chr17:76477663 (GRCh38)
- Gene constraint
- LOEUF 0.545 · pLI 0.15 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.53 · 5 PDB
- Residue 265
- the 'involved in interaction with frmd8' region
Similar variants
- RHBDF2 p.Ile157Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- RHBDF2 c.151-27G>T Uncertain significance ★★ ⚠ same type
- RHBDF2 c.151-86G>A Uncertain significance ★★ ⚠ same type
- RHBDF2 p.Ala397Ser Uncertain significance ★★ ⚠ same type
- RHBDF2 p.Ala700Thr Uncertain significance ★★ ⚠ same type
- RHBDF2 p.Ala725Val Uncertain significance ★★ ⚠ same type
- RHBDF2 p.Arg113His Uncertain significance ★★ ⚠ same type
- RHBDF2 p.Arg205His 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/rhbdf2-p-phe265 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown