Is SLC32A1 p.Gly26Val (c.77G>T) pathogenic?

SLC32A1 p.Gly26Val (c.77G>T) is classified Uncertain significance in SLC32A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-20). AlphaMissense: ambiguous (0.3789); Ultra-rare (popmax 0.0356%, eas); Associated with Inborn genetic diseases.

What condition is associated with SLC32A1 p.Gly26Val (c.77G>T)?

SLC32A1 p.Gly26Val (c.77G>T) is associated with Inborn genetic diseases (ClinVar).

How common is SLC32A1 p.Gly26Val (c.77G>T) in the general population?

SLC32A1 p.Gly26Val (c.77G>T) is ultra-rare (popmax 0.0356%, eas) (gnomAD).

What do computational predictors say about SLC32A1 p.Gly26Val (c.77G>T)?

AlphaMissense predicts ambiguous (score 0.3789) — an in-silico prediction, not a clinical call.

SLC32A1 p.Gly26Val

c.77G>T · rs766274199 · VCV3164282

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3789 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0356%, eas)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3789	ambiguous
REVEL	0.261	benign-leaning
SaProt	LLR -8.38	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.4, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 312 bp · p 0.28 · regional, not allelic
Overall
CADD	24.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0356% East Asian · 16/44,888 alleles

Filtering AF 0.0223% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0182%

Overall 0.00105% 17/1,613,948 alleles · ultra-rare exomes 14/1,461,558 · genomes 3/152,390 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0356%	2,805
Remaining individualsnot grpmax-eligible	0.0016%	62,490

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: SLC32A1
Protein: p.Gly26Val
Coding: c.77G>T
MANE Select: NM_080552
dbSNP: rs766274199
Type: single nucleotide variant
Location: chr20:38724801 (GRCh38)
Gene constraint: LOEUF 0.396 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 78.69

Full SLC32A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SLC32A1 p.Ser225Cys Uncertain significance ★★ ⚠ same condition
SLC32A1 p.Ala168Ser Uncertain significance ★ ⚠ same condition
SLC32A1 p.Ala22Thr Uncertain significance ★ ⚠ same condition
SLC32A1 p.Ala75Ser Uncertain significance ★ ⚠ same condition
SLC32A1 p.Arg197His Uncertain significance ★ ⚠ same condition
SLC32A1 p.Arg415Ser Uncertain significance ★ ⚠ same condition
SLC32A1 p.Arg483Cys Uncertain significance ★ ⚠ same condition
SLC32A1 p.Arg483Ser 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/slc32a1-p-gly26val (accessed [today's date]).

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