HTR2B p.Pro278=
c.834G>A · rs115328679 · VCV725269
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.233%, afr)
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 -0.67 | GERP -3.7 |
| Overall | ||
| CADD | 5.459 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.233%
African / African-American · 175/75,046 alleles
Filtering AF
0.205%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.194%
Overall
0.0156%
251/1,614,040 alleles · rare
exomes 137/1,461,748 · genomes 114/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.233% | 429 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,167 |
| South Asian | 0.011% | 9,108 |
| Admixed American | 0.00833% | 12,005 |
| East Asian | 0.00446% | 22,440 |
| European (non-Finnish) | 0.00373% | 26,816 |
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
- HTR2B
- Protein
- p.Pro278=
- Coding
- c.834G>A
- MANE Select
- NM_000867
- dbSNP
- rs115328679
- Type
- single nucleotide variant
- Location
- chr2:231109129 (GRCh38)
- Gene constraint
- LOEUF 1.004 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.48 · 15 PDB
Similar variants
- HTR2B p.Asn438= Benign ★★ same type
- HTR2B p.Gly51Glu Benign ★★ same type
- HTR2B p.Met421Val Benign ★★ same type
- HTR2B p.Trp31Arg Benign ★★ same type
- HTR2B p.Val208Leu Benign ★★ same type
- HTR2B p.Ala282Pro Uncertain significance ★ ⚠ same type
- HTR2B p.Ala401Ser Uncertain significance ★ ⚠ same type
- HTR2B p.Ala97Val 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/htr2b-p-pro278 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown