HTR2A p.Ser17=
c.51C>T · rs150684157 · VCV731446
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.221%, 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 3.4 | GERP -0.041, phastCons 1 |
| Overall | ||
| CADD | 11.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.221%
African / African-American · 166/75,016 alleles
Filtering AF
0.194%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.183%
Overall
0.011%
177/1,613,780 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.221% | 452 |
| Middle Eastern | 0.033% | 3,029 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| Admixed American | 0.00333% | 30,003 |
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
- HTR2A
- Protein
- p.Ser17=
- Coding
- c.51C>T
- MANE Select
- NM_000621
- dbSNP
- rs150684157
- Type
- single nucleotide variant
- Location
- chr13:46895856 (GRCh38)
- Gene constraint
- LOEUF 0.632 · pLI 0.36 (gnomAD)
- Structure
- AlphaFold pLDDT 74.03 · 47 PDB
Similar variants
- HTR2A p.Ala447Val Likely benign ★★ same type
- HTR2A p.Leu229= Benign/Likely benign ★★ same type
- HTR2A p.Ser219= Likely benign ★★ same type
- HTR2A p.Ser34= Likely benign ★★ same type
- HTR2A p.Ser62= Likely benign ★★ same type
- HTR2A c.412+1G>C Uncertain significance ★ same type
- HTR2A p.Ala230Thr Uncertain significance ★ ⚠ same type
- HTR2A p.Ala447Thr 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/htr2a-p-ser17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown