CDX2

caudal type homeobox 2, the group of HOXL subclass homeoboxes

Basic information

Region (hg38): 13:27960918-27969315

Previous symbols: [ "CDX3" ]

Links

ENSG00000165556 ∙ NCBI:1045 ∙ OMIM:600297 ∙ HGNC:1806 ∙ Uniprot:Q99626 ∙ 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 CDX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDX2 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		1	27			28
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	1	28	0	1

Variants in CDX2

This is a list of pathogenic ClinVar variants found in the CDX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-27963117-A-G		Sirenomelia	Likely pathogenic (Feb 12, 2020)
13-27963122-G-C		not specified	Uncertain significance (Mar 20, 2023)
13-27963141-C-T		not specified	Uncertain significance (Jan 30, 2024)
13-27963180-G-G			Benign (Feb 18, 2019)
13-27963207-G-A		not specified	Uncertain significance (Aug 12, 2021)
13-27963208-A-T		not specified	Uncertain significance (Mar 29, 2024)
13-27963296-T-G		not specified	Uncertain significance (Aug 18, 2021)
13-27963335-T-C		Anorectal malformation	Conflicting classifications of pathogenicity (Oct 07, 2024)
13-27963375-A-T			Likely benign (Apr 19, 2018)
13-27964892-G-A		not specified	Uncertain significance (Nov 15, 2023)
13-27964932-G-A		not specified	Uncertain significance (Dec 05, 2024)
13-27968469-G-T		not specified	Uncertain significance (Jan 01, 2025)
13-27968471-C-T		not specified	Uncertain significance (Sep 14, 2023)
13-27968493-G-A			Uncertain significance (Aug 06, 2024)
13-27968519-C-T		not specified	Uncertain significance (Jul 05, 2024)
13-27968528-C-T		not specified	Uncertain significance (May 24, 2023)
13-27968589-G-C		not specified	Uncertain significance (Aug 20, 2024)
13-27968627-G-T		not specified	Uncertain significance (Aug 28, 2024)
13-27968639-G-A		not specified	Uncertain significance (Nov 23, 2024)
13-27968664-G-T		not specified	Uncertain significance (Nov 21, 2022)
13-27968665-A-C		not specified	Uncertain significance (Dec 12, 2023)
13-27968672-T-G		not specified	Uncertain significance (Jan 03, 2025)
13-27968673-C-T		not specified	Uncertain significance (Oct 03, 2022)
13-27968700-C-A		not specified	Uncertain significance (Oct 24, 2023)
13-27968725-G-T		not specified	Uncertain significance (Jul 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDX2	protein_coding	protein_coding	ENST00000381020	3	9003

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.529	0.468	125489	0	2	125491	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	126	164	0.768	0.00000796	1963
Missense in Polyphen		20	34.752	0.57551		417
Synonymous	-0.672	83	75.6	1.10	0.00000386	665
Loss of Function	2.46	2	10.7	0.187	4.62e-7	115

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000660	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine. Binds preferentially to methylated DNA (PubMed:28473536). {ECO:0000269|PubMed:28473536}.
• Pathway: Gastric cancer - Homo sapiens (human);Vitamin D Receptor Pathway;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;Preimplantation Embryo;Developmental Biology;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;Transcriptional regulation of pluripotent stem cells (Consensus)

Recessive Scores

• pRec: 0.551

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.900
• hipred: Y
• hipred_score: 0.761
• ghis: 0.408

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.737

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdx2
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; neoplasm; digestive/alimentary phenotype; limbs/digits/tail phenotype; skeleton phenotype; embryo 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); 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); normal phenotype; reproductive system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;blood vessel development;trophectodermal cell differentiation;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;positive regulation of cell population proliferation;endosome to lysosome transport;animal organ morphogenesis;anterior/posterior axis specification;anterior/posterior pattern specification;regulation of somitogenesis;cell differentiation;somatic stem cell population maintenance;establishment or maintenance of epithelial cell apical/basal polarity;positive regulation of cell differentiation;positive regulation of transcription, DNA-templated;intestinal epithelial cell differentiation;labyrinthine layer development
• Cellular component: condensed nuclear chromosome;nucleus;nucleoplasm;transcriptional repressor complex
• 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 repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;methyl-CpG binding