Is UBA1 p.Ser511= (c.1533A>G) pathogenic?

UBA1 p.Ser511= (c.1533A>G) is classified Likely benign in UBA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-03-15). Absent from gnomAD v4.1; Associated with infantile-onset X-linked spinal muscular atrophy.

What condition is associated with UBA1 p.Ser511= (c.1533A>G)?

UBA1 p.Ser511= (c.1533A>G) is associated with infantile-onset X-linked spinal muscular atrophy (ClinVar).

How common is UBA1 p.Ser511= (c.1533A>G) in the general population?

UBA1 p.Ser511= (c.1533A>G) is absent from gnomAD v4.1 (gnomAD).

How is Infantile-onset X-linked spinal muscular atrophy inherited?

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

UBA1 p.Ser511=

c.1533A>G · rs2147263778 · VCV1079446

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

infantile-onset X-linked spinal muscular atrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Overall
CADD	7.923	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: UBA1
Protein: p.Ser511=
Coding: c.1533A>G
MANE Select: NM_003334
dbSNP: rs2147263778
Type: single nucleotide variant
Location: chrX:47203654 (GRCh38)
Structure: AlphaFold pLDDT 92.71 · 11 PDB
Residue 511: the '2 approximate repeats' region; an α-helix

Full UBA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

infantile-onset X-linked spinal muscular atrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Infantile-onset X-linked spinal muscular atrophy (Orphanet):

Inheritance: X-linked recessive
Onset: Neonatal

Similar variants

UBA1 c.910-9C>G Uncertain significance ★★ same condition
UBA1 p.Ala136Ser Uncertain significance ★★ ⚠ same condition
UBA1 p.Ala391Thr Uncertain significance ★★ ⚠ same condition
UBA1 p.Arg288His Uncertain significance ★★ ⚠ same condition
UBA1 p.Arg345Gln Uncertain significance ★★ ⚠ same condition
UBA1 p.Arg544Trp Uncertain significance ★★ ⚠ same condition
UBA1 p.Arg693Cys Uncertain significance ★★ ⚠ same condition
UBA1 p.Arg699Gln Uncertain significance ★★ ⚠ 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/uba1-p-ser511 (accessed [today's date]).

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