RHAG p.Ser367=
c.1101C>T · rs139371066 · VCV2435427
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0801%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.05 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.35 | GERP -3.5, phastCons 0.65 |
| Overall | ||
| CADD | 3.112 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0801%
African / African-American · 60/74,908 alleles
Filtering AF
0.0638%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.058%
Overall
0.00415%
67/1,613,702 alleles · ultra-rare
exomes 39/1,461,544 · genomes 28/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0801% | 1,248 |
| Admixed American | 0.00834% | 11,987 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,237 |
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.Ser367=
- Coding
- c.1101C>T
- MANE Select
- NM_000324
- dbSNP
- rs139371066
- Type
- single nucleotide variant
- Location
- chr6:49607187 (GRCh38)
- Gene constraint
- LOEUF 0.728 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.44 · 8 PDB
- Residue 367
- 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-ser367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown