Is CP p.Thr31= (c.93G>A) pathogenic?

CP p.Thr31= (c.93G>A) is classified Conflicting classifications of pathogenicity in CP (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-01-24). Rare (popmax 0.281%, mid); Associated with aceruloplasminemia.

What condition is associated with CP p.Thr31= (c.93G>A)?

CP p.Thr31= (c.93G>A) is associated with aceruloplasminemia (ClinVar).

How common is CP p.Thr31= (c.93G>A) in the general population?

CP p.Thr31= (c.93G>A) is rare (popmax 0.281%, mid) (gnomAD).

How is Aceruloplasminemia inherited?

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

CP p.Thr31=

c.93G>A · rs201521886 · VCV343791

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.281%, mid)

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 -0.31	GERP -3.8
Overall
CADD	7.197	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.281% Middle Eastern · 17/6,056 alleles

Filtering AF 0.179% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.147%

Overall 0.016% 258/1,613,120 alleles · rare exomes 238/1,460,868 · genomes 20/152,252 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.281%	356
Ashkenazi Jewishnot grpmax-eligible	0.098%	1,020
Remaining individualsnot grpmax-eligible	0.0432%	2,314
Admixed American	0.0317%	3,153
South Asian	0.0176%	5,668
European (non-Finnish)	0.0123%	8,135
African / African-American	0.00667%	14,998

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.Thr31=
Coding: c.93G>A
MANE Select: NM_000096
dbSNP: rs201521886
Type: single nucleotide variant
Location: chr3:149221700 (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 31: the plastocyanin-like 1 domain; a β-strand

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 p.Thr31Met Uncertain significance ★★ ⚠ same residue
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

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-thr31 (accessed [today's date]).

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