HTR2A p.Leu157=
c.471C>G · rs909805204 · VCV2643809
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 1.5 | GERP 0.3, phastCons 1 |
| Overall | ||
| CADD | 6.829 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,024 alleles
Overall
6.84e-05%
1/1,461,888 alleles · very rare
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.Leu157=
- Coding
- c.471C>G
- MANE Select
- NM_000621
- dbSNP
- rs909805204
- Type
- single nucleotide variant
- Location
- chr13:46892532 (GRCh38)
- Gene constraint
- LOEUF 0.632 · pLI 0.36 (gnomAD)
- Structure
- AlphaFold pLDDT 74.03 · 47 PDB
- Residue 157
- a disulfide bond; an α-helix
Similar variants
- HTR2A p.Ala447Val Likely benign ★★ same type
- HTR2A p.Leu229= Benign/Likely benign ★★ same type
- HTR2A p.Ser17= 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
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-leu157 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown