Is UBA1 p.Pro797= (c.2391C>T) pathogenic?

UBA1 p.Pro797= (c.2391C>T) is classified Likely benign in UBA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-26). Ultra-rare (popmax 0.0123%, sas); Associated with infantile-onset X-linked spinal muscular atrophy.

What condition is associated with UBA1 p.Pro797= (c.2391C>T)?

UBA1 p.Pro797= (c.2391C>T) is associated with infantile-onset X-linked spinal muscular atrophy (ClinVar).

How common is UBA1 p.Pro797= (c.2391C>T) in the general population?

UBA1 p.Pro797= (c.2391C>T) is ultra-rare (popmax 0.0123%, sas) (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.Pro797=

c.2391C>T · rs1556793279 · VCV1572639

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0123%, sas)

Conditions

infantile-onset X-linked spinal muscular atrophy

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 -15	GERP -3.1
Overall
CADD	2.395	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0123% South Asian · 7/57,012 alleles

Filtering AF 0.00569% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00407%

Overall 0.00116% 14/1,211,676 alleles · ultra-rare exomes 14/1,097,945 · genomes 0/113,731 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0123%	8,145
East Asian	0.00295%	33,844
Admixed American	0.00217%	46,071
European (non-Finnish)	0.000558%	179,111

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: UBA1
Protein: p.Pro797=
Coding: c.2391C>T
MANE Select: NM_003334
dbSNP: rs1556793279
Type: single nucleotide variant
Location: chrX:47211152 (GRCh38)
Structure: AlphaFold pLDDT 92.71 · 11 PDB
Residue 797: 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-pro797 (accessed [today's date]).

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