Is GAL p.Ala47= (c.141C>T) pathogenic?

GAL p.Ala47= (c.141C>T) is classified Likely benign in GAL (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-19). Ultra-rare (popmax 0.0134%, afr); Associated with familial temporal lobe epilepsy 8.

What condition is associated with GAL p.Ala47= (c.141C>T)?

GAL p.Ala47= (c.141C>T) is associated with familial temporal lobe epilepsy 8 (ClinVar).

How common is GAL p.Ala47= (c.141C>T) in the general population?

GAL p.Ala47= (c.141C>T) is ultra-rare (popmax 0.0134%, afr) (gnomAD).

GAL p.Ala47=

c.141C>T · rs367644530 · VCV1133243

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, afr)

Conditions

familial temporal lobe epilepsy 8

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.27	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -0.74	GERP -2.8
Overall
CADD	14.92	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% African / African-American · 10/74,780 alleles

Filtering AF 0.00724% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00551%

Overall 0.000933% 15/1,607,074 alleles · ultra-rare exomes 5/1,454,864 · genomes 10/152,210 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0134%	7,478
Remaining individualsnot grpmax-eligible	0.00321%	31,114
European (non-Finnish)	0.000256%	391,337

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: GAL
Protein: p.Ala47=
Coding: c.141C>T
MANE Select: NM_015973
dbSNP: rs367644530
Type: single nucleotide variant
Location: chr11:68688018 (GRCh38)
Structure: AlphaFold pLDDT 66.71

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

Disease context

familial temporal lobe epilepsy 8 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GAL p.Ala47Val Uncertain significance ★ same residue
GAL p.Ala10Thr Uncertain significance ★★ ⚠ same condition
GAL p.Ala15Thr Uncertain significance ★★ ⚠ same condition
GAL p.Arg67Trp Uncertain significance ★★ ⚠ same condition
GAL p.Arg88His Uncertain significance ★★ ⚠ same condition
GAL p.Asp106Asn Uncertain significance ★★ ⚠ same condition
GAL p.Asp106His Uncertain significance ★★ ⚠ same condition
GAL p.Glu69Lys 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/gal-p-ala47 (accessed [today's date]).

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