CDX1

caudal type homeobox 1, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 5:150166778-150184558

Links

ENSG00000113722 ∙ NCBI:1044 ∙ OMIM:600746 ∙ HGNC:1805 ∙ Uniprot:P47902 ∙ 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 CDX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDX1 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			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	0

Variants in CDX1

This is a list of pathogenic ClinVar variants found in the CDX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-150166890-A-G		not specified	Uncertain significance (Sep 03, 2024)
5-150166926-C-A		not specified	Uncertain significance (Sep 25, 2023)
5-150166938-C-T		not specified	Uncertain significance (May 17, 2023)
5-150166968-G-T		not specified	Uncertain significance (Feb 19, 2025)
5-150166988-G-C		not specified	Uncertain significance (Dec 03, 2021)
5-150167016-G-C		not specified	Uncertain significance (Aug 01, 2022)
5-150167046-C-T		not specified	Uncertain significance (Sep 27, 2021)
5-150167092-G-C		not specified	Uncertain significance (Aug 30, 2021)
5-150167121-C-T		not specified	Uncertain significance (Dec 22, 2023)
5-150167186-C-T		not specified	Uncertain significance (Nov 07, 2023)
5-150167195-C-T		not specified	Uncertain significance (Jun 07, 2023)
5-150167223-T-A		not specified	Uncertain significance (Nov 14, 2024)
5-150167303-G-A		not specified	Uncertain significance (Aug 05, 2015)
5-150167306-G-A		CDX1-related disorder	Uncertain significance (Jul 31, 2023)
5-150167310-G-A		not specified	Uncertain significance (Mar 14, 2023)
5-150182768-G-A		not specified	Uncertain significance (Aug 07, 2023)
5-150182776-C-T		not specified	Uncertain significance (Oct 29, 2021)
5-150182797-G-A		not specified	Uncertain significance (Apr 19, 2023)
5-150182813-A-C		not specified	Uncertain significance (Feb 27, 2025)
5-150182819-G-A		not specified	Uncertain significance (Mar 31, 2024)
5-150182839-T-A		not specified	Uncertain significance (Apr 09, 2024)
5-150182867-G-T		not specified	Uncertain significance (Apr 20, 2023)
5-150182869-C-T		not specified	Uncertain significance (Dec 15, 2023)
5-150182870-G-A		not specified	Uncertain significance (Nov 09, 2024)
5-150182896-G-A		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDX1	protein_coding	protein_coding	ENST00000231656	3	17763

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.143	0.786	125418	0	2	125420	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0641	99	101	0.982	0.00000684	1613
Missense in Polyphen		39	46.038	0.84713		691
Synonymous	0.765	37	43.4	0.852	0.00000276	579
Loss of Function	1.46	2	5.80	0.345	2.49e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000681	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000882
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in transcriptional regulation (PubMed:24623306). Involved in activated KRAS-mediated transcriptional activation of PRKD1 in colorectal cancer (CRC) cells (PubMed:24623306). Binds to the PRKD1 promoter in colorectal cancer (CRC) cells (PubMed:24623306). Could play a role in the terminal differentiation of the intestine. Binds preferentially to methylated DNA (PubMed:28473536). {ECO:0000269|PubMed:24623306, ECO:0000269|PubMed:28473536}.
• Pathway: Regulation of nuclear beta catenin signaling and target gene transcription (Consensus)

Recessive Scores

• pRec: 0.196

Haploinsufficiency Scores

• pHI: 0.321
• hipred: N
• hipred_score: 0.424
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00721

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdx1
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); craniofacial phenotype; cellular phenotype; embryo phenotype; pigmentation phenotype; normal phenotype; hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: cdx1b
• Affected structure: intestinal epithelial cell
• Phenotype tag: abnormal
• Phenotype quality: cuboid

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;animal organ morphogenesis;anterior/posterior axis specification;anterior/posterior pattern specification;regulation of somitogenesis;cell differentiation;positive regulation of transcription by RNA polymerase II;bone morphogenesis
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II distal enhancer 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;methyl-CpG binding;transcription regulatory region DNA binding