CDX4

caudal type homeobox 4, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): X:73447052-73455171

Links

ENSG00000131264 ∙ NCBI:1046 ∙ OMIM:300025 ∙ HGNC:1808 ∙ Uniprot:O14627 ∙ 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 CDX4 gene.

• Inborn genetic diseases (11 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDX4 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			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in CDX4

This is a list of pathogenic ClinVar variants found in the CDX4 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-73447370-G-A		not specified	Likely benign (May 17, 2023)
X-73447371-C-A		not specified	Conflicting classifications of pathogenicity (Feb 16, 2023)
X-73447407-C-T		not specified	Uncertain significance (Aug 02, 2021)
X-73447419-T-C		not specified	Uncertain significance (Jan 23, 2024)
X-73447453-C-A			Likely benign (Mar 29, 2018)
X-73447474-C-T		not specified	Uncertain significance (Dec 14, 2022)
X-73447566-C-A		not specified	Uncertain significance (Apr 06, 2022)
X-73447614-G-T		not specified	Uncertain significance (Dec 28, 2022)
X-73447806-G-C		CDX4-related disorder	Likely benign (Jul 04, 2023)
X-73453565-A-G		not specified	Uncertain significance (Dec 17, 2023)
X-73453594-T-C		not specified	Uncertain significance (Mar 21, 2022)
X-73453658-G-C		not specified	Uncertain significance (Jun 24, 2022)
X-73454385-A-C		not specified	Uncertain significance (Jan 03, 2024)
X-73454407-C-G		not specified	Uncertain significance (Dec 16, 2022)
X-73454425-T-C		not specified	Uncertain significance (Dec 17, 2023)
X-73454443-A-T		not specified	Uncertain significance (Jun 07, 2023)
X-73454526-C-T		not specified	Uncertain significance (Jul 27, 2022)
X-73454538-C-T		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDX4	protein_coding	protein_coding	ENST00000373514	3	7992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00602	0.749	125721	10	10	125741	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0984	120	123	0.975	0.00000985	1852
Missense in Polyphen		44	39.647	1.1098		723
Synonymous	0.446	50	54.2	0.923	0.00000507	574
Loss of Function	0.846	4	6.29	0.636	4.33e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000211	0.000149
Middle Eastern	0.00	0.00
South Asian	0.000179	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Regulation of nuclear beta catenin signaling and target gene transcription (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.430
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.277
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000408

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdx4
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; limbs/digits/tail phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: cdx4
• Affected structure: podocyte
• Phenotype tag: abnormal
• Phenotype quality: mislocalised posteriorly

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;blood vessel development;regulation of transcription by RNA polymerase II;anterior/posterior axis specification;anterior/posterior pattern specification;cell differentiation;positive regulation of transcription by RNA polymerase II;labyrinthine layer development
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding