Is UBA2 p.Met1Val (c.1A>G) pathogenic?

UBA2 p.Met1Val (c.1A>G) is classified Pathogenic/Likely pathogenic in UBA2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-13). No allele count reported in gnomAD v4.1 (AN 1,266,450); Associated with Inborn genetic diseases.

What condition is associated with UBA2 p.Met1Val (c.1A>G)?

UBA2 p.Met1Val (c.1A>G) is associated with Inborn genetic diseases (ClinVar).

How common is UBA2 p.Met1Val (c.1A>G) in the general population?

UBA2 p.Met1Val (c.1A>G) is no allele count reported in gnomAD v4.1 (AN 1,266,450) (gnomAD).

UBA2 p.Met1Val

c.1A>G · rs2075210211 · VCV985243

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

start-loss

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,266,450)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	start-loss	predicted loss-of-function in a LoF-intolerant gene
REVEL	0.158	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.6, phastCons 1
Overall
CADD	21.5	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,266,450). 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: UBA2
Protein: p.Met1Val
Coding: c.1A>G
MANE Select: NM_005499
dbSNP: rs2075210211
Type: single nucleotide variant
Location: chr19:34428433 (GRCh38)
Gene constraint: LOEUF 0.258 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 85.72 · 16 PDB

Full UBA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

UBA2 p.Arg274Trp Uncertain significance ★★ ⚠ same condition
UBA2 p.Ile468Leu Uncertain significance ★★ ⚠ same condition
UBA2 p.Ala121Thr Uncertain significance ★ ⚠ same condition
UBA2 p.Ala215Val Uncertain significance ★ ⚠ same condition
UBA2 p.Ala296Val Uncertain significance ★ ⚠ same condition
UBA2 p.Ala559Thr Uncertain significance ★ ⚠ same condition
UBA2 p.Ala622Gly Uncertain significance ★ ⚠ same condition
UBA2 p.Ala87Pro 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/uba2-p-met1val (accessed [today's date]).

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