Is CP p.Cys13= (c.39T>C) pathogenic?

CP p.Cys13= (c.39T>C) is classified Likely benign in CP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-03-14). Very rare (popmax 0.00167%, amr); Associated with CP-related disorder.

What condition is associated with CP p.Cys13= (c.39T>C)?

CP p.Cys13= (c.39T>C) is associated with CP-related disorder (ClinVar).

How common is CP p.Cys13= (c.39T>C) in the general population?

CP p.Cys13= (c.39T>C) is very rare (popmax 0.00167%, amr) (gnomAD).

CP p.Cys13=

c.39T>C · rs551624643 · VCV3029760

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

CP-related disorder

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 1.3	GERP 0.75
Overall
CADD	4.671	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,010 alleles

Overall 0.000657% 1/152,278 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: CP
Protein: p.Cys13=
Coding: c.39T>C
MANE Select: NM_000096
dbSNP: rs551624643
Type: single nucleotide variant
Location: chr3:149221754 (GRCh38)
Gene constraint: LOEUF 0.624 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.79 · 4 PDB

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

Disease context

CP-related disorder

Similar variants

CP p.Ser121Ter Likely pathogenic ★ same condition
CP p.Trp230Ter Pathogenic ★ same condition
CP p.Trp644Ter Likely pathogenic ★ same condition
CP p.Lys753Ter Likely pathogenic same condition
CP p.Tyr1011Ter Pathogenic same condition
CP p.Val996Ala Uncertain significance ⚠ same condition
CP p.Glu380fs Likely pathogenic ★ same condition
CP c.1208+1G>A Pathogenic ★★ same type

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-cys13 (accessed [today's date]).

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