HTR2C p.Ser167=
c.501G>A · VCV3352450
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00296%, eas)
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 1.4 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 9.929 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00296%
East Asian · 1/33,814 alleles
Filtering AF
0.000105%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.1e-05%
Overall
0.000496%
6/1,210,562 alleles · very rare
exomes 6/1,097,046 · genomes 0/113,516 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00296% | 33,814 |
| Admixed American | 0.00218% | 45,887 |
| European (non-Finnish) | 0.000447% | 223,675 |
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.Ser167=
- Coding
- c.501G>A
- MANE Select
- NM_000868
- Type
- single nucleotide variant
- Location
- chrX:114848154 (GRCh38)
- Structure
- AlphaFold pLDDT 73.71 · 8 PDB
- Residue 167
- an α-helix
Disease context
HTR2C-related disorder
Similar variants
- 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
- HTR2C p.Asn166Ser 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-ser167 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown