ATP7B p.Ser391=
c.1173G>C · rs200431213 · VCV2860748
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Wilson disease
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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6 | GERP -4 |
| Overall | ||
| CADD | 0.067 | 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
- ATP7B
- Protein
- p.Ser391=
- Coding
- c.1173G>C
- MANE Select
- NM_000053
- dbSNP
- rs200431213
- Type
- single nucleotide variant
- Location
- chr13:51974047 (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 391
- the hma 4 domain; a β-strand
Disease context
Wilson disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Wilson disease (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Elderly
- Prevalence
- 1-9 / 100 000 (Worldwide)
Similar variants
- ATP7B p.Ser391Pro Uncertain significance ★★ ⚠ same residue
- ATP7B p.Ser391Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- ATP7B p.Ser391fs Pathogenic/Likely pathogenic ★★ same residue
- ATP7B c.1285+2T>A Pathogenic/Likely pathogenic ★★ same condition
- ATP7B c.1286-2A>G Pathogenic ★★ same condition
- ATP7B c.1543+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ATP7B c.1543+1G>C Pathogenic ★★ same condition
- ATP7B c.1544-2A>G 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-ser391 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown