RHAG p.Phe313=
c.939C>T · rs1409270348 · VCV1693912
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00305%, 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 1.4 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 1.741 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00305%
European (non-Finnish) · 36/1,180,008 alleles
Filtering AF
0.00223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.00223%
36/1,614,130 alleles · very rare
exomes 36/1,461,834 · genomes 0/152,296 · 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
- RHAG
- Protein
- p.Phe313=
- Coding
- c.939C>T
- MANE Select
- NM_000324
- dbSNP
- rs1409270348
- Type
- single nucleotide variant
- Location
- chr6:49612403 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.44 · 8 PDB
- Residue 313
- an α-helix
Similar variants
- RHAG c.157+1G>A Pathogenic/Likely pathogenic ★★ same type
- RHAG p.Phe65Ser Pathogenic ★★ same type
- RHAG c.341+4A>G Uncertain significance ★★ same type
- RHAG p.Arg191Gln Uncertain significance ★★ ⚠ same type
- RHAG p.Arg264Gln Uncertain significance ★★ ⚠ same type
- RHAG p.Glu49Gln Uncertain significance ★★ ⚠ same type
- RHAG p.His325Arg Uncertain significance ★★ ⚠ same type
- RHAG p.Ile146Thr 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/rhag-p-phe313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown