Is HTR2C p.Val30= (c.90A>G) pathogenic?

HTR2C p.Val30= (c.90A>G) is classified Likely benign in HTR2C (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-07-11). Very rare (popmax 0.00176%, afr); Associated with HTR2C-related disorder.

What condition is associated with HTR2C p.Val30= (c.90A>G)?

HTR2C p.Val30= (c.90A>G) is associated with HTR2C-related disorder (ClinVar).

How common is HTR2C p.Val30= (c.90A>G) in the general population?

HTR2C p.Val30= (c.90A>G) is very rare (popmax 0.00176%, afr) (gnomAD).

HTR2C p.Val30=

c.90A>G · VCV3355239

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00176%, afr)

Conditions

HTR2C-related disorder

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 2.3	GERP -3.8, phastCons 1
Overall
CADD	4.751	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00176% African / African-American · 1/56,658 alleles

Overall 8.3e-05% 1/1,204,200 alleles · very rare exomes 0/1,093,573 · genomes 1/110,627 · joint denominator

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.Val30=
Coding: c.90A>G
MANE Select: NM_000868
Type: single nucleotide variant
Location: chrX:114731348 (GRCh38)
Structure: AlphaFold pLDDT 73.71 · 8 PDB

Full HTR2C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-val30 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown