Is HTT p.Ala2646Thr (c.7936G>A) pathogenic?

HTT p.Ala2646Thr (c.7936G>A) is classified Uncertain significance in HTT (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-07). AlphaMissense: likely benign (0.0585); Ultra-rare (popmax 0.0464%, sas).

How common is HTT p.Ala2646Thr (c.7936G>A) in the general population?

HTT p.Ala2646Thr (c.7936G>A) is ultra-rare (popmax 0.0464%, sas) (gnomAD).

What do computational predictors say about HTT p.Ala2646Thr (c.7936G>A)?

AlphaMissense predicts likely benign (score 0.0585) — an in-silico prediction, not a clinical call.

HTT p.Ala2646Thr

c.7936G>A · rs555039658 · VCV1443501

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0585 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0464%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Computational evidence

Protein change
AlphaMissense	0.0585	likely benign
REVEL	0.015	strongly benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP -3.6
Overall
CADD	5.401	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0464% South Asian · 42/90,582 alleles

Filtering AF 0.0352% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0313%

Overall 0.00385% 62/1,608,666 alleles · ultra-rare exomes 56/1,456,420 · genomes 6/152,246 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0464%	2,157
Remaining individualsnot grpmax-eligible	0.00643%	15,557
African / African-American	0.00134%	74,860
European (non-Finnish)	0.00127%	78,459

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: HTT
Protein: p.Ala2646Thr
Coding: c.7936G>A
MANE Select: NM_001388492
dbSNP: rs555039658
Type: single nucleotide variant
Location: chr4:3228702 (GRCh38)
Structure: AlphaFold pLDDT 85.38 · 30 PDB

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

Similar variants

HTT p.Ala2646= Benign/Likely benign ★★ same residue
HTT c.889+6G>T Uncertain significance ★★ same type
HTT p.Ala2739Thr Uncertain significance ★★ same type
HTT p.Arg1654Trp Uncertain significance ★★ same type
HTT p.Arg1945Trp Uncertain significance ★★ same type
HTT p.Asp1157Gly Uncertain significance ★★ same type
HTT p.Asp920Asn Uncertain significance ★★ same type
HTT p.Glu449Ala 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/htt-p-ala2646thr (accessed [today's date]).

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