Is CP p.Lys770= (c.2310G>A) pathogenic?

CP p.Lys770= (c.2310G>A) is classified Conflicting classifications of pathogenicity in CP (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2025-11-12). Ultra-rare (popmax 0.0599%, sas); Associated with aceruloplasminemia.

What condition is associated with CP p.Lys770= (c.2310G>A)?

CP p.Lys770= (c.2310G>A) is associated with aceruloplasminemia (ClinVar).

How common is CP p.Lys770= (c.2310G>A) in the general population?

CP p.Lys770= (c.2310G>A) is ultra-rare (popmax 0.0599%, sas) (gnomAD).

How is Aceruloplasminemia inherited?

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

CP p.Lys770=

c.2310G>A · rs553883583 · VCV343757

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0599%, sas)

Conditions

aceruloplasminemia

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 -0.11	GERP 0.12, phastCons 0.005
Overall
CADD	9.135	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0599% South Asian · 54/90,108 alleles

Filtering AF 0.0471% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0426%

Overall 0.00663% 106/1,599,874 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0599%	1,669
Middle Eastern	0.0173%	5,776
Remaining individualsnot grpmax-eligible	0.00806%	12,406
European (non-Finnish)	0.00384%	26,009
Ashkenazi Jewishnot grpmax-eligible	0.00339%	29,488

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: CP
Protein: p.Lys770=
Coding: c.2310G>A
MANE Select: NM_000096
dbSNP: rs553883583
Type: single nucleotide variant
Location: chr3:149183581 (GRCh38)
Gene constraint: LOEUF 0.624 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.79 · 4 PDB
Residue 770: the plastocyanin-like 5 domain

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

Disease context

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

For Aceruloplasminemia (Orphanet):

Inheritance: Autosomal recessive
Onset: Adult, Elderly
Prevalence: 1-9 / 1 000 000 (Japan)

Similar variants

CP c.1208+1G>A Pathogenic ★★ same condition
CP c.2879-1G>T Likely pathogenic ★★ same condition
CP p.Arg901Ter Pathogenic ★★ same condition
CP p.Gly195Arg Likely pathogenic ★★ same condition
CP p.Gly650Arg Pathogenic/Likely pathogenic ★★ same condition
CP p.Gly708Ser Pathogenic ★★ same condition
CP p.Leu919Pro Pathogenic/Likely pathogenic ★★ same condition
CP p.Val219Glu 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/cp-p-lys770 (accessed [today's date]).

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