Is BCAT1 p.Thr13= (c.39C>T) pathogenic?

BCAT1 p.Thr13= (c.39C>T) is classified Benign in BCAT1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-05-31). Low-frequency (popmax 3.43%, mid).

How common is BCAT1 p.Thr13= (c.39C>T) in the general population?

BCAT1 p.Thr13= (c.39C>T) is low-frequency (popmax 3.43%, mid) (gnomAD).

BCAT1 p.Thr13=

c.39C>T · rs17374606 · VCV718749

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.43%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -11	GERP -3
Overall
CADD	0.086	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.43% Middle Eastern · 208/6,062 alleles

Filtering AF 3.05% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.9%

Overall 0.736% 11,878/1,613,872 alleles · low-frequency

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	3.47%	29
Middle Easterngrpmax	3.43%	29
Finnishnot grpmax-eligible	2.38%	42
Remaining individualsnot grpmax-eligible	1.07%	93
European (non-Finnish)	0.653%	153
South Asian	0.468%	214
Amishnot grpmax-eligible	0.439%	228
Admixed American	0.318%	314
African / African-American	0.159%	630
East Asian	0.0111%	8,975

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: BCAT1
Protein: p.Thr13=
Coding: c.39C>T
MANE Select: NM_005504
dbSNP: rs17374606
Type: single nucleotide variant
Location: chr12:24901853 (GRCh38)
Gene constraint: LOEUF 1.219 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.05 · 17 PDB

Full BCAT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BCAT1 c.7-1070G>A Uncertain significance ★ same type
BCAT1 c.7-1075C>T Uncertain significance ★ same type
BCAT1 c.7-1078C>T Uncertain significance ★ same type
BCAT1 c.7-1082G>T Uncertain significance ★ same type
BCAT1 c.7-1091C>T Uncertain significance ★ same type
BCAT1 p.Ala27Thr Uncertain significance ★ ⚠ same type
BCAT1 p.Ala298Thr Uncertain significance ★ ⚠ same type
BCAT1 p.Arg122Cys 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/bcat1-p-thr13 (accessed [today's date]).

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