RHOXF2 p.Ser62=
c.186G>A · rs374278020 · VCV2661315
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0278%, 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 0.79 | phastCons 0.004 |
| Overall | ||
| CADD | 2.501 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0278%
European (non-Finnish) · 248/891,061 alleles
Filtering AF
0.0249%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0239%
Overall
0.022%
264/1,199,051 alleles · ultra-rare
exomes 249/1,094,712 · genomes 15/104,339 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0278% | 3,593 |
| Remaining individualsnot grpmax-eligible | 0.019% | 5,253 |
| African / African-American | 0.00552% | 18,105 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00457% | 21,873 |
| Finnishnot grpmax-eligible | 0.00439% | 22,776 |
| East Asian | 0.00299% | 33,419 |
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
- RHOXF2
- Protein
- p.Ser62=
- Coding
- c.186G>A
- MANE Select
- NM_032498
- dbSNP
- rs374278020
- Type
- single nucleotide variant
- Location
- chrX:120159121 (GRCh38)
- Structure
- AlphaFold pLDDT 64.38
- Residue 62
- the 'disordered' region
Similar variants
- RHOXF2 p.Ala124Thr Uncertain significance ★ ⚠ same type
- RHOXF2 p.Ala133Gly Uncertain significance ★ ⚠ same type
- RHOXF2 p.Ala133Thr Uncertain significance ★ ⚠ same type
- RHOXF2 p.Arg120His Uncertain significance ★ ⚠ same type
- RHOXF2 p.Arg164Gly Uncertain significance ★ ⚠ same type
- RHOXF2 p.Asn137Asp Uncertain significance ★ ⚠ same type
- RHOXF2 p.Glu111Asp Uncertain significance ★ ⚠ same type
- RHOXF2 p.Glu150Gly 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/rhoxf2-p-ser62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown