CPXCR1

CPX chromosome region candidate 1

Basic information

Region (hg38): X:88747225-88754785

Links

ENSG00000147183 ∙ NCBI:53336 ∙ OMIM:301055 ∙ HGNC:2332 ∙ Uniprot:Q8N123 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPXCR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPXCR1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			19	3	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	2

Variants in CPXCR1

This is a list of pathogenic ClinVar variants found in the CPXCR1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-88753482-C-T		not specified	Uncertain significance (Mar 04, 2025)
X-88753493-T-G		not specified	Uncertain significance (Jul 09, 2024)
X-88753499-A-G		not specified	Uncertain significance (Apr 29, 2024)
X-88753510-G-T		not specified	Uncertain significance (Oct 27, 2021)
X-88753511-T-C		not specified	Likely benign (Oct 27, 2021)
X-88753625-G-A		not specified	Uncertain significance (Feb 01, 2025)
X-88753656-G-A		not specified	Conflicting classifications of pathogenicity (Jul 14, 2024)
X-88753719-C-A			Benign (Jun 18, 2018)
X-88753784-T-A			Likely benign (Jun 18, 2018)
X-88753815-T-A		not specified	Uncertain significance (Feb 23, 2023)
X-88753824-C-T		not specified	Uncertain significance (Aug 27, 2024)
X-88753880-C-G		not specified	Uncertain significance (Aug 11, 2022)
X-88753922-A-C		not specified	Uncertain significance (Apr 12, 2023)
X-88753938-G-A		not specified	Likely benign (Aug 03, 2022)
X-88753943-T-C		not specified	Uncertain significance (Mar 14, 2023)
X-88753944-A-G		not specified	Uncertain significance (Jul 17, 2024)
X-88753950-C-G		not specified	Uncertain significance (Sep 26, 2024)
X-88753989-G-C		not specified	Uncertain significance (Aug 21, 2024)
X-88754030-C-T		not specified	Uncertain significance (Sep 29, 2023)
X-88754091-A-G		not specified	Uncertain significance (Jun 22, 2023)
X-88754105-G-C		not specified	Uncertain significance (Feb 07, 2025)
X-88754165-A-G		not specified	Uncertain significance (Aug 16, 2022)
X-88754169-G-C			Benign (Mar 05, 2018)
X-88754177-G-C		not specified	Uncertain significance (Nov 09, 2024)
X-88754202-T-C		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPXCR1	protein_coding	protein_coding	ENST00000276127	1	7561

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.563	118	102	1.16	0.00000723	1993
Missense in Polyphen		26	17.971	1.4468		342
Synonymous	-0.190	37	35.6	1.04	0.00000253	564
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0363

Intolerance Scores

• loftool: 0.654
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.02

Haploinsufficiency Scores

• pHI: 0.0219
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000748

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cpxcr1

Gene ontology

• Molecular function: nucleic acid binding