Is ARSA p.Arg82fs (c.244del) pathogenic?

ARSA p.Arg82fs (c.244del) is classified Pathogenic/Likely pathogenic in ARSA (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-02-14). Absent from gnomAD; Associated with metachromatic leukodystrophy.

What condition is associated with ARSA p.Arg82fs (c.244del)?

ARSA p.Arg82fs (c.244del) is associated with metachromatic leukodystrophy (ClinVar).

How common is ARSA p.Arg82fs (c.244del) in the general population?

ARSA p.Arg82fs (c.244del) is absent from gnomAD (gnomAD).

How is Metachromatic leukodystrophy inherited?

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

ARSA p.Arg82fs

c.244del · rs1569081823 · VCV633043

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

metachromatic leukodystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ARSA
Protein: p.Arg82fs
Coding: c.244del
MANE Select: NM_000487
dbSNP: rs1569081823
Type: Deletion
Location: chr22:50627387 (GRCh38)
Gene constraint: LOEUF 1.166 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.43 · 10 PDB
Residue 82: an α-helix; a UniProt-annotated variant site (in mld; late-infantile-onset)

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 p.Arg82Gln Pathogenic/Likely pathogenic ★★ same residue
ARSA p.Arg82Trp Pathogenic/Likely pathogenic ★★ same residue
ARSA p.Arg82Leu Pathogenic ★ same residue
ARSA c.979_979+3del Pathogenic/Likely pathogenic ★★ same condition
ARSA p.Ala12fs Pathogenic ★★ same condition
ARSA p.Ala5fs Pathogenic ★★ same condition
ARSA p.Arg21fs Pathogenic/Likely pathogenic ★★ same condition
ARSA p.Asp37fs 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-arg82fs (accessed [today's date]).

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