Is GNPAT p.Arg352= (c.1056A>G) pathogenic?

GNPAT p.Arg352= (c.1056A>G) is classified Likely benign in GNPAT (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-13). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with GNPAT p.Arg352= (c.1056A>G)?

GNPAT p.Arg352= (c.1056A>G) is associated with Inborn genetic diseases (ClinVar).

How common is GNPAT p.Arg352= (c.1056A>G) in the general population?

GNPAT p.Arg352= (c.1056A>G) is absent from gnomAD v4.1 (gnomAD).

GNPAT p.Arg352=

c.1056A>G · rs2527028630 · VCV3100666

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.082	GERP -3.9, phastCons 0.011
Overall
CADD	9.19	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: GNPAT
Protein: p.Arg352=
Coding: c.1056A>G
MANE Select: NM_014236
dbSNP: rs2527028630
Type: single nucleotide variant
Location: chr1:231267680 (GRCh38)
Gene constraint: LOEUF 0.572 · pLI 0.88 (gnomAD)
Structure: AlphaFold pLDDT 88.96

Full GNPAT 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

GNPAT p.Ala206Ser Uncertain significance ★★ ⚠ same condition
GNPAT p.Arg115His Uncertain significance ★★ ⚠ same condition
GNPAT p.Arg202Gln Uncertain significance ★★ ⚠ same condition
GNPAT p.Arg515Cys Uncertain significance ★★ ⚠ same condition
GNPAT p.Arg515His Uncertain significance ★★ ⚠ same condition
GNPAT p.Arg518His Uncertain significance ★★ ⚠ same condition
GNPAT p.Asp190Glu Uncertain significance ★★ ⚠ same condition
GNPAT p.Cys122Tyr 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/gnpat-p-arg352 (accessed [today's date]).

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