Is SPR c.596del pathogenic?

SPR c.596del is classified Pathogenic in SPR (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-18). No gnomAD frequency available for this variant; Associated with dopa-responsive dystonia due to sepiapterin reductase deficiency.

What condition is associated with SPR c.596del?

SPR c.596del is associated with dopa-responsive dystonia due to sepiapterin reductase deficiency (ClinVar).

How common is SPR c.596del in the general population?

SPR c.596del is no gnomAD frequency available for this variant (gnomAD).

SPR c.596del

Q: How is Dopa-responsive dystonia due to sepiapterin reductase deficiency inherited?

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

rs1553498582 · VCV522878

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

dopa-responsive dystonia due to sepiapterin reductase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.7, phastCons 1
Non-coding constraint	Z 3.92	1 kb window · o/e 0.73 · regional · uncalibrated

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: SPR
Coding: c.596del
MANE Select: NM_003124
dbSNP: rs1553498582
Type: Deletion
Location: chr2:72891346 (GRCh38)
Gene constraint: LOEUF 1.528 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.71 · 14 PDB

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

Disease context

dopa-responsive dystonia due to sepiapterin reductase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Dopa-responsive dystonia due to sepiapterin reductase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

SPR c.596-2_602del Pathogenic/Likely pathogenic ★★ same condition
SPR p.Leu222fs Pathogenic/Likely pathogenic ★★ same condition
SPR c.304+2_304+13del Pathogenic ★ same condition
SPR p.Glu211fs Likely pathogenic same condition
SPR p.Thr151fs Pathogenic same condition
SPR p.Ile98del Uncertain significance same condition
SPR p.Arg150Gly Pathogenic ★★ same condition
SPR p.Arg219Ter 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/spr-c-596del (accessed [today's date]).

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