Is HTT p.Met1360Ile (c.4080G>A) pathogenic?

HTT p.Met1360Ile (c.4080G>A) is classified Likely benign in HTT (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-30). AlphaMissense: likely pathogenic (0.9267); Absent from gnomAD v4.1; Associated with HTT-related disorder.

What condition is associated with HTT p.Met1360Ile (c.4080G>A)?

HTT p.Met1360Ile (c.4080G>A) is associated with HTT-related disorder (ClinVar).

How common is HTT p.Met1360Ile (c.4080G>A) in the general population?

HTT p.Met1360Ile (c.4080G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about HTT p.Met1360Ile (c.4080G>A)?

AlphaMissense predicts likely pathogenic (score 0.9267) — an in-silico prediction, not a clinical call.

HTT p.Met1360Ile

c.4080G>A · rs2476129770 · VCV3040819

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9267 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

HTT-related disorder

Computational evidence

Protein change
AlphaMissense	0.9267	likely pathogenic
REVEL	0.43	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.2, phastCons 1
Overall
CADD	27.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: HTT
Protein: p.Met1360Ile
Coding: c.4080G>A
MANE Select: NM_001388492
dbSNP: rs2476129770
Type: single nucleotide variant
Location: chr4:3173045 (GRCh38)
Structure: AlphaFold pLDDT 85.38 · 30 PDB

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

Disease context

HTT-related disorder

Similar variants

HTT p.Phe1142= Likely benign ★★ same condition
HTT p.Pro2946= Likely benign ★★ same condition
HTT p.Val2008= Likely benign ★★ same condition
HTT p.Ala1089= Benign ★ same condition
HTT p.Ala2022= Likely benign ★ same condition
HTT p.Ala229Val Likely benign ★ same condition
HTT p.Ala2338= Likely benign ★ same condition
HTT p.Ala2644= Benign ★ 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/htt-p-met1360ile (accessed [today's date]).

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