Is GOT1 p.Ala13Val (c.38C>T) pathogenic?

GOT1 p.Ala13Val (c.38C>T) is classified Uncertain significance in GOT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-16). AlphaMissense: ambiguous (0.5153); Very rare (popmax 0.000255%, nfe).

How common is GOT1 p.Ala13Val (c.38C>T) in the general population?

GOT1 p.Ala13Val (c.38C>T) is very rare (popmax 0.000255%, nfe) (gnomAD).

What do computational predictors say about GOT1 p.Ala13Val (c.38C>T)?

AlphaMissense predicts ambiguous (score 0.5153) — an in-silico prediction, not a clinical call.

GOT1 p.Ala13Val

c.38C>T · rs1458717877 · VCV2336097

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5153 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000255%, nfe)

Computational evidence

Protein change
AlphaMissense	0.5153	ambiguous
REVEL	0.3	indeterminate
SaProt	LLR -9.47	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.9	GERP 1.9, phastCons 1
Overall
CADD	23.8	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 0.000255% European (non-Finnish) · 3/1,177,480 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000186% 3/1,609,608 alleles · very rare exomes 1/1,457,384 · genomes 2/152,224 · 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: GOT1
Protein: p.Ala13Val
Coding: c.38C>T
MANE Select: NM_002079
dbSNP: rs1458717877
Type: single nucleotide variant
Location: chr10:99430528 (GRCh38)
Structure: AlphaFold pLDDT 88.17

Full GOT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GOT1 c.643-5C>T Benign/Likely benign ★★ same type
GOT1 p.Glu183Gly Benign ★★ ⚠ same type
GOLT1B p.Gly100Asp Uncertain significance ★ ⚠ same type
GOLT1B p.Gly132Ala Uncertain significance ★ ⚠ same type
GOLT1B p.Leu41Ile Uncertain significance ★ ⚠ same type
GOLT1B p.Lys64Asn Uncertain significance ★ ⚠ same type
GOLT1B p.Phe56Cys Uncertain significance ★ ⚠ same type
GOLT1B p.Pro83Leu 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/got1-p-ala13val (accessed [today's date]).

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