Is ARG1 p.Val47= (c.141G>A) pathogenic?

ARG1 p.Val47= (c.141G>A) is classified Likely benign in ARG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-07). Absent from gnomAD v4.1; Associated with arginase deficiency.

What condition is associated with ARG1 p.Val47= (c.141G>A)?

ARG1 p.Val47= (c.141G>A) is associated with arginase deficiency (ClinVar).

How common is ARG1 p.Val47= (c.141G>A) in the general population?

ARG1 p.Val47= (c.141G>A) is absent from gnomAD v4.1 (gnomAD).

How is Argininemia inherited?

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

ARG1 p.Val47=

c.141G>A · rs2482351228 · VCV2846330

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

arginase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.8	GERP 0.69, phastCons 1
Overall
CADD	7.221	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: ARG1
Protein: p.Val47=
Coding: c.141G>A
MANE Select: NM_004830 · reported on NM_000045
dbSNP: rs2482351228
Type: single nucleotide variant
Location: chr6:131579121 (GRCh38)

Full ARG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

arginase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Argininemia (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy
Prevalence: <1 / 1 000 000 (Finland)

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/arg1-p-val47 (accessed [today's date]).

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