HTR2C p.Ala7=
c.21G>A · rs202034357 · VCV3038696
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0749%, sas)
Conditions
1
HTR2C-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.009 | GERP 2.3 |
| Overall | ||
| CADD | 4.809 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0749%
South Asian · 34/45,419 alleles
Filtering AF
0.055%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0482%
Overall
0.0112%
125/1,112,110 alleles · ultra-rare
exomes 116/1,000,743 · genomes 9/111,367 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0749% | 1,336 |
| Remaining individualsnot grpmax-eligible | 0.0114% | 8,756 |
| African / African-American | 0.00958% | 10,440 |
| Admixed American | 0.00946% | 10,572 |
| European (non-Finnish) | 0.00906% | 11,037 |
| East Asian | 0.00337% | 29,704 |
| Finnishnot grpmax-eligible | 0.00219% | 45,720 |
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
- HTR2C
- Protein
- p.Ala7=
- Coding
- c.21G>A
- MANE Select
- NM_000868
- dbSNP
- rs202034357
- Type
- single nucleotide variant
- Location
- chrX:114726957 (GRCh38)
- Structure
- AlphaFold pLDDT 73.71 · 8 PDB
Disease context
HTR2C-related disorder
Similar variants
- HTR2C p.Ala7Val Likely benign ★ same residue
- HTR2C p.Val8= Uncertain significance ★ same condition
- HTR2C c.349+2T>C Uncertain significance same condition
- HTR2C p.Arg288Ter Uncertain significance same condition
- HTR2C p.Arg295Cys Uncertain significance ⚠ same condition
- HTR2C p.Arg295Gly Uncertain significance ⚠ same condition
- HTR2C p.Arg400Ser Uncertain significance ⚠ same condition
- HTR2C p.Arg454Met Uncertain significance ⚠ same condition
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/htr2c-p-ala7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown