Is GNPTAB p.Arg68= (c.204G>C) pathogenic?

GNPTAB p.Arg68= (c.204G>C) is classified Likely benign in GNPTAB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-15). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with GNPTAB p.Arg68= (c.204G>C)?

GNPTAB p.Arg68= (c.204G>C) is associated with Inborn genetic diseases (ClinVar).

How common is GNPTAB p.Arg68= (c.204G>C) in the general population?

GNPTAB p.Arg68= (c.204G>C) is absent from gnomAD v4.1 (gnomAD).

GNPTAB p.Arg68=

c.204G>C · VCV4620985

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	—	not assessed · no allele here is in the release
Pangolin	Δ0.28	loss · gain 0.03 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 2.5	GERP 2.4, phastCons 1
Overall
CADD	17.06	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: GNPTAB
Protein: p.Arg68=
Coding: c.204G>C
MANE Select: NM_024312
Type: single nucleotide variant
Location: chr12:101790057 (GRCh38)
Gene constraint: LOEUF 0.8 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.15 · 5 PDB
Residue 68: an α-helix

Full GNPTAB 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

GNPTAB p.Arg68Gln Uncertain significance ★★ ⚠ same residue
GNPTAB p.Arg68Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
GNPTAB p.Gln205Ter Pathogenic/Likely pathogenic ★★ same condition
GNPTAB p.Ala1234Thr Uncertain significance ★★ ⚠ same condition
GNPTAB p.Asn524Asp Uncertain significance ★★ ⚠ same condition
GNPTAB p.Asp193Gly Uncertain significance ★★ ⚠ same condition
GNPTAB p.Asp407Asn Uncertain significance ★★ ⚠ same condition
GNPTAB p.Gln1006His 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/gnptab-p-arg68 (accessed [today's date]).

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