Is ARSA p.Val328Met (c.982G>A) pathogenic?

ARSA p.Val328Met (c.982G>A) is classified Likely benign in ARSA (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-04). Rare (popmax 0.351%, eas); Associated with metachromatic leukodystrophy.

What condition is associated with ARSA p.Val328Met (c.982G>A)?

ARSA p.Val328Met (c.982G>A) is associated with metachromatic leukodystrophy (ClinVar).

How common is ARSA p.Val328Met (c.982G>A) in the general population?

ARSA p.Val328Met (c.982G>A) is rare (popmax 0.351%, eas) (gnomAD).

How is Metachromatic leukodystrophy inherited?

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

ARSA p.Val328Met

c.982G>A · rs143994992 · VCV728267

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.351%, eas)

Conditions

metachromatic leukodystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.788	moderately pathogenic-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 2.2, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 2,631 bp · p 0.96 · regional, not allelic
Overall
CADD	26.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.351% East Asian · 155/44,114 alleles

Filtering AF 0.306% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.289%

Overall 0.0139% 221/1,595,018 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.351%	285
Remaining individualsnot grpmax-eligible	0.0307%	3,262
Middle Eastern	0.0166%	6,032
African / African-American	0.00667%	14,996
South Asian	0.0057%	17,537
Ashkenazi Jewishnot grpmax-eligible	0.00344%	29,108
European (non-Finnish)	0.0029%	34,499
Admixed American	0.00181%	55,324

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: ARSA
Protein: p.Val328Met
Coding: c.982G>A
MANE Select: NM_000487
dbSNP: rs143994992
Type: single nucleotide variant
Location: chr22:50626061 (GRCh38)
Gene constraint: LOEUF 1.166 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.43 · 10 PDB
Residue 328: a disulfide bond

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

Disease context

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

For Metachromatic leukodystrophy (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

ARSA c.1107+1G>A Pathogenic/Likely pathogenic ★★ same condition
ARSA c.1107+1G>T Pathogenic ★★ same condition
ARSA c.1108-2A>G Pathogenic ★★ same condition
ARSA c.1108-3C>G Pathogenic/Likely pathogenic ★★ same condition
ARSA c.1210+1G>A Pathogenic ★★ same condition
ARSA c.224+1G>A Likely pathogenic ★★ same condition
ARSA c.225-1G>C Likely pathogenic ★★ same condition
ARSA c.225-2A>G 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/arsa-p-val328met (accessed [today's date]).

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