HTR2A p.Ser62=
c.186A>C · rs1190153612 · VCV736153
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.133%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.27 | acceptor loss, 31 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.5 | GERP -3.9 |
| Overall | ||
| CADD | 5.725 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.133%
European (non-Finnish) · 1,555/1,171,260 alleles
Filtering AF
0.127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.125%
Overall
0.109%
1,744/1,604,058 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.133% | 753 |
| Remaining individualsnot grpmax-eligible | 0.0869% | 1,150 |
| Middle Eastern | 0.0828% | 1,208 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0678% | 1,476 |
| South Asian | 0.0495% | 2,020 |
| African / African-American | 0.0495% | 2,021 |
| East Asian | 0.0246% | 4,063 |
| Finnishnot grpmax-eligible | 0.0172% | 5,807 |
| Admixed American | 0.01% | 9,993 |
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.Ser62=
- Coding
- c.186A>C
- MANE Select
- NM_000621
- dbSNP
- rs1190153612
- Type
- single nucleotide variant
- Location
- chr13:46895721 (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.Ser17= Benign ★★ same type
- HTR2A p.Ser219= Likely benign ★★ same type
- HTR2A p.Ser34= 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-ser62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown