Is ATP7B p.Val1298del (c.3889GTC[1]) pathogenic?

ATP7B p.Val1298del (c.3889GTC[1]) is classified Pathogenic in ATP7B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2000-01-01). Very rare (popmax 8.47e-05%, nfe); Associated with Wilson disease.

What condition is associated with ATP7B p.Val1298del (c.3889GTC[1])?

ATP7B p.Val1298del (c.3889GTC[1]) is associated with Wilson disease (ClinVar).

How common is ATP7B p.Val1298del (c.3889GTC[1]) in the general population?

ATP7B p.Val1298del (c.3889GTC[1]) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

How is Wilson disease inherited?

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

ATP7B p.Val1298del

c.3889GTC[1] · rs2138570625 · VCV3854

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

Wilson disease

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.9	GERP 1.1, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,020 alleles

Overall 6.84e-05% 1/1,461,720 alleles · very rare

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: ATP7B
Protein: p.Val1298del
Coding: c.3889GTC[1]
MANE Select: NM_000053
dbSNP: rs2138570625
Type: Microsatellite
Location: chr13:51937485 (GRCh38)
Gene constraint: LOEUF 1.063 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 71.83 · 13 PDB
Residue 1298: a UniProt-annotated variant site (in wd; uncertain significance); a β-strand

Full ATP7B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For Wilson disease (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Elderly
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

ATP7B p.Val1298Ile Uncertain significance ★★ ⚠ same residue
ATP7B p.Val1298= Likely benign ★★ same residue
ATP7B p.Arg414fs Pathogenic ★★ same condition
ATP7B p.Ile930del Pathogenic/Likely pathogenic ★★ same condition
ATP7B p.Leu745fs Pathogenic/Likely pathogenic ★★ same condition
ATP7B p.Lys1248fs Pathogenic ★★ same condition
ATP7B p.Val1024fs Pathogenic ★★ same condition
ATP7B p.Val1187fs Pathogenic/Likely pathogenic ★★ 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/atp7b-p-val1298del (accessed [today's date]).

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