Is ATP7B p.Cys985= (c.2955C>T) pathogenic?

ATP7B p.Cys985= (c.2955C>T) is classified Conflicting classifications of pathogenicity in ATP7B (ClinVar, Conflicting submitters, 16 submitters; last evaluated 2026-03-01). Rare (popmax 0.737%, afr); Associated with Inborn genetic diseases.

What condition is associated with ATP7B p.Cys985= (c.2955C>T)?

ATP7B p.Cys985= (c.2955C>T) is associated with Inborn genetic diseases, Wilson disease (ClinVar).

How common is ATP7B p.Cys985= (c.2955C>T) in the general population?

ATP7B p.Cys985= (c.2955C>T) is rare (popmax 0.737%, afr) (gnomAD).

ATP7B p.Cys985=

c.2955C>T · rs116587608 · VCV285883

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 16 submitters

gnomAD v4.1

Rare

rare (popmax 0.737%, afr)

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
Constraint at this position
Conservation	phyloP 3.3	GERP -4, phastCons 1
Overall
CADD	9.065	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.737% African / African-American · 553/75,064 alleles

Filtering AF 0.686% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.666%

Overall 0.04% 646/1,613,986 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.737%	136
Remaining individualsnot grpmax-eligible	0.0528%	1,894
Admixed American	0.0433%	2,309
European (non-Finnish)	0.00288%	34,707

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.Cys985=
Coding: c.2955C>T
MANE Select: NM_000053
dbSNP: rs116587608
Type: single nucleotide variant
Location: chr13:51946389 (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 985: a UniProt-annotated variant site (in wd); an α-helix

Full ATP7B 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

Also linked: Wilson disease

Similar variants

ATP7B p.Cys985Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
ATP7B p.Cys985fs Pathogenic ★★ same residue
ATP7B p.Cys985Tyr Uncertain significance ★ ⚠ 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-cys985 (accessed [today's date]).

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