CPXCR1

protein-coding

CPX chromosome region candidate 1

Gene summary

This gene is one of several genes identified in a region of the X chromosome associated with an X-linked cleft palate (CPX) disorder. The encoded protein contains a motif similar to a motif found in zinc-finger proteins. Mutation analysis of this gene has not revealed any mutation which causes the CPX disorder. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Sep 2011]

MANE transcript

NM_033048.6

Inheritance

—

ClinVar variants

U:32B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:88,747,225-88,754,785

External References & Databases

Ensembl (ENSG00000147183)

Transcript & Mutation Effects

hg38 • Region Span ~7.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CPXCR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033048.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			32 clinvar	5 clinvar	2 clinvar	39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	5	2	39

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033048.6	RefSeq	NP_149037.5	1	MANE Select
ENST00000276127.9	Ensembl	ENSP00000276127.4	1	MANE Select
NM_001184771.2	RefSeq	NP_001171700.2	1	Standard
ENST00000373111.5	Ensembl	ENSP00000362203.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

nucleic acid binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000276127
Coding exons: 1
Length: 7561

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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0363

Intolerance Scores

LoFtool: 0.654
RVIS EVS: 0.88
RVIS percentile EVS: 89.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.000748

Gene Damage Prediction

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