RFX7 p.Pro20Ser
c.58C>T · rs536003334 · VCV2355591
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00917%, afr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.041 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.46 | GERP -2.1, phastCons 0.92 |
| Regional constraint | o/e 0.98 | unconstrained · MANE · 140 kb · p 0.82 · regional, not allelic |
| Overall | ||
| CADD | 19.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00917%
African / African-American · 6/65,410 alleles
Filtering AF
0.00399%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00266%
Overall
0.000984%
13/1,321,410 alleles · very rare
exomes 5/1,175,978 · genomes 8/145,432 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00917% | 10,902 |
| East Asian | 0.0052% | 19,222 |
| Finnishnot grpmax-eligible | 0.00255% | 39,246 |
| European (non-Finnish) | 0.0005% | 200,029 |
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
- RFX7
- Protein
- p.Pro20Ser
- Coding
- c.58C>T
- MANE Select
- NM_022841
- dbSNP
- rs536003334
- Type
- single nucleotide variant
- Location
- chr15:56243228 (GRCh38)
- Gene constraint
- LOEUF 0.3 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 43.61 · 2 PDB
- Residue 20
- the 'disordered' region
Similar variants
- RFX7 p.Pro700Ser Uncertain significance ★★ ⚠ same condition
- RFX7 p.Ser100Cys Uncertain significance ★★ same condition
- RFX7 p.Ser1070Thr Uncertain significance ★★ ⚠ same condition
- RFX7 p.Ser974Asn Uncertain significance ★★ ⚠ same condition
- RFX7 p.Val1127Leu Uncertain significance ★★ same condition
- RFX7 p.Ala425Thr Likely benign ★★ same condition
- RFX7 p.Ile1384Thr Likely benign ★★ same condition
- RFX7 p.Met1033Thr Likely benign ★★ same condition
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/rfx7-p-pro20ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown