Is GALC p.Asp110= (c.330C>T) pathogenic?

GALC p.Asp110= (c.330C>T) is classified Benign/Likely benign in GALC (ClinVar, Multiple submitters, 12 submitters; last evaluated 2026-02-04). Low-frequency (popmax 4.58%, nfe); Associated with Krabbe disease.

What condition is associated with GALC p.Asp110= (c.330C>T)?

GALC p.Asp110= (c.330C>T) is associated with Krabbe disease (ClinVar).

How common is GALC p.Asp110= (c.330C>T) in the general population?

GALC p.Asp110= (c.330C>T) is low-frequency (popmax 4.58%, nfe) (gnomAD).

How is Krabbe disease inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

GALC p.Asp110=

c.330C>T · rs11552556 · VCV92502

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 12 submitters

gnomAD v4.1

Rare

low-frequency (popmax 4.58%, nfe)

Conditions

Krabbe disease

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.59 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.9	GERP -1.2, phastCons 1
Overall
CADD	13.54	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.58% European (non-Finnish) · 53,592/1,169,460 alleles

Filtering AF 4.55% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.54%

Overall 4% 64,127/1,602,176 alleles · low-frequency

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	5.37%	19
Finnishnot grpmax-eligible	5.24%	19
Ashkenazi Jewishnot grpmax-eligible	4.99%	20
European (non-Finnish)grpmax	4.58%	22
Remaining individualsnot grpmax-eligible	3.34%	30
South Asian	2.12%	47
Admixed American	1.73%	58
Middle Eastern	1.54%	65
African / African-American	0.699%	143
East Asian	0.0335%	2,987

Amish 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: GALC
Protein: p.Asp110=
Coding: c.330C>T
MANE Select: NM_000153
dbSNP: rs11552556
Type: single nucleotide variant
Location: chr14:87986601 (GRCh38)
Gene constraint: LOEUF 1.019 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.56

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

Disease context

Krabbe disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Krabbe disease (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (United States)

Similar variants

GALC p.Asp110Asn Uncertain significance ★ ⚠ same residue
GALC p.Asp110His Uncertain significance ★ ⚠ same residue
GALC c.1033+1G>A Likely pathogenic ★★ same condition
GALC c.1034-1G>C Pathogenic/Likely pathogenic ★★ same condition
GALC c.1034-2A>G Pathogenic/Likely pathogenic ★★ same condition
GALC c.1161+2T>A Likely pathogenic ★★ same condition
GALC c.1251+1G>C Pathogenic/Likely pathogenic ★★ same condition
GALC c.1252-1G>C Pathogenic/Likely pathogenic ★★ 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/galc-p-asp110 (accessed [today's date]).

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