CXXC4

CXXC finger protein 4, the group of Zinc fingers CXXC-type

Basic information

Region (hg38): 4:104468307-104494901

Links

ENSG00000168772 ∙ NCBI:80319 ∙ OMIM:611645 ∙ HGNC:24593 ∙ Uniprot:Q9H2H0 ∙ 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 CXXC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXXC4 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				7		7
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	7	0

Variants in CXXC4

This is a list of pathogenic ClinVar variants found in the CXXC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-104490962-G-A		not specified	Uncertain significance (Dec 21, 2023)
4-104491171-C-G		not specified	Uncertain significance (May 24, 2023)
4-104491244-C-G		not specified	Uncertain significance (Aug 12, 2021)
4-104491250-G-A		not specified	Uncertain significance (Apr 20, 2024)
4-104491253-A-G		not specified	Uncertain significance (Apr 04, 2024)
4-104491410-A-C			Likely benign (Dec 01, 2022)
4-104491413-A-C			Likely benign (Feb 01, 2024)
4-104491419-G-C			Likely benign (Nov 01, 2022)
4-104491452-A-C			Likely benign (Feb 01, 2024)
4-104491458-C-G			Likely benign (Oct 01, 2023)
4-104491464-G-C			Likely benign (Jan 01, 2023)
4-104491467-G-C			Likely benign (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXXC4	protein_coding	protein_coding	ENST00000394767	2	26590

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.889	0.110	125731	0	2	125733	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	107	175	0.613	0.00000813	2350
Missense in Polyphen		19	58.5	0.32479		710
Synonymous	-2.03	99	76.4	1.30	0.00000381	808
Loss of Function	2.47	0	7.13	0.00	3.04e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a negative regulator of the Wnt signaling pathway via its interaction with DVL1. {ECO:0000250}.
• Pathway: Wnt signaling pathway - Homo sapiens (human);Wnt Signaling Pathway;Signaling by WNT;Signal Transduction;Negative regulation of TCF-dependent signaling by DVL-interacting proteins;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.536
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cxxc4

Gene ontology

• Biological process: zygotic specification of dorsal/ventral axis;Wnt signaling pathway;negative regulation of Wnt signaling pathway
• Cellular component: cytoplasm;cytoplasmic vesicle
• Molecular function: DNA binding;zinc ion binding;PDZ domain binding