Is HTT p.Arg2663Trp (c.7987C>T) pathogenic?

HTT p.Arg2663Trp (c.7987C>T) is classified Uncertain significance in HTT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-14). AlphaMissense: ambiguous (0.4799); Very rare (popmax 0.00975%, nfe).

How common is HTT p.Arg2663Trp (c.7987C>T) in the general population?

HTT p.Arg2663Trp (c.7987C>T) is very rare (popmax 0.00975%, nfe) (gnomAD).

What do computational predictors say about HTT p.Arg2663Trp (c.7987C>T)?

AlphaMissense predicts ambiguous (score 0.4799) — an in-silico prediction, not a clinical call.

HTT p.Arg2663Trp

c.7987C>T · rs765523847 · VCV1424382

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4799 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00975%, nfe)

Computational evidence

Protein change
AlphaMissense	0.4799	ambiguous
REVEL	0.418	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 1.6, phastCons 1
Overall
CADD	33.0	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

Grpmax group 0.00975% European (non-Finnish) · 115/1,179,040 alleles

Filtering AF 0.00826% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00775%

Overall 0.00738% 119/1,612,750 alleles · very rare exomes 108/1,460,664 · genomes 11/152,086 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00975%	10,253
Remaining individualsnot grpmax-eligible	0.0032%	31,218
South Asian	0.0022%	45,526

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.Arg2663Trp
Coding: c.7987C>T
MANE Select: NM_001388492
dbSNP: rs765523847
Type: single nucleotide variant
Location: chr4:3228887 (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 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
HTT p.Gly2084Arg 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-arg2663trp (accessed [today's date]).

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