Is SPAST p.Pro33= (c.99T>A) pathogenic?

SPAST p.Pro33= (c.99T>A) is classified Likely benign in SPAST (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Very rare (popmax 0.000264%, nfe); Associated with hereditary spastic paraplegia 4.

What condition is associated with SPAST p.Pro33= (c.99T>A)?

SPAST p.Pro33= (c.99T>A) is associated with hereditary spastic paraplegia 4 (ClinVar).

How common is SPAST p.Pro33= (c.99T>A) in the general population?

SPAST p.Pro33= (c.99T>A) is very rare (popmax 0.000264%, nfe) (gnomAD).

How is Autosomal dominant spastic paraplegia type 4 inherited?

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

SPAST p.Pro33=

c.99T>A · rs1573027124 · VCV763234

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000264%, nfe)

Conditions

hereditary spastic paraplegia 4

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP -2, phastCons 0.99
Overall
CADD	12.03	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000264% European (non-Finnish) · 3/1,135,500 alleles

Filtering AF 7e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 2e-05%

Overall 0.000194% 3/1,548,012 alleles · very rare exomes 3/1,397,204 · genomes 0/150,808 · joint denominator

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: SPAST
Protein: p.Pro33=
Coding: c.99T>A
MANE Select: NM_014946
dbSNP: rs1573027124
Type: single nucleotide variant
Location: chr2:32063930 (GRCh38)
Gene constraint: LOEUF 0.69 · pLI 0.11 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.03 · 7 PDB
Residue 33: the 'required for interaction with rtn1' region; the 'required for midbody localization' region; the 'required for interaction with atl1' region; the 'required for nuclear localization' region; the 'disordered' region

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

Disease context

hereditary spastic paraplegia 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal dominant spastic paraplegia type 4 (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 1 000 000 (Portugal)

Similar variants

SPAST p.Pro33Leu Uncertain significance ★★ ⚠ same residue
SPAST p.Pro33Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
SPAST p.Pro33Ser Uncertain significance ★ ⚠ same residue
SPAST p.Pro33_Ala35del Uncertain significance ★★ same residue
SPAST c.1004+1G>C Pathogenic/Likely pathogenic ★★ same condition
SPAST c.1004+1G>T Pathogenic ★★ same condition
SPAST c.1004+2T>G Pathogenic ★★ same condition
SPAST c.1098+1G>A 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/spast-p-pro33 (accessed [today's date]).

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