CXXC5

CXXC finger protein 5, the group of Zinc fingers CXXC-type

Basic information

Region (hg38): 5:139647299-139683882

Links

ENSG00000171604 ∙ NCBI:51523 ∙ OMIM:612752 ∙ HGNC:26943 ∙ Uniprot:Q7LFL8 ∙ 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 CXXC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXXC5 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				1		1
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in CXXC5

This is a list of pathogenic ClinVar variants found in the CXXC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-139680528-C-T		not specified	Uncertain significance (Mar 19, 2024)
5-139680536-G-A		not specified	Uncertain significance (Dec 16, 2022)
5-139680546-C-A		not specified	Uncertain significance (Nov 03, 2022)
5-139680557-G-A		not specified	Uncertain significance (Aug 26, 2022)
5-139680560-G-A		not specified	Uncertain significance (Dec 04, 2023)
5-139680563-A-G		not specified	Uncertain significance (Jan 09, 2025)
5-139680591-G-A		not specified	Uncertain significance (Aug 20, 2024)
5-139680630-A-G		not specified	Uncertain significance (Jan 28, 2025)
5-139680634-G-C		not specified	Uncertain significance (Dec 30, 2024)
5-139680656-G-A		not specified	Likely benign (Aug 12, 2021)
5-139680681-C-T		not specified	Uncertain significance (Mar 07, 2025)
5-139680687-C-A		not specified	Uncertain significance (Sep 26, 2023)
5-139680687-C-T		not specified	Uncertain significance (Dec 24, 2024)
5-139680690-C-A		not specified	Uncertain significance (Jan 04, 2024)
5-139680711-G-T		not specified	Uncertain significance (Dec 25, 2024)
5-139680716-A-C		not specified	Uncertain significance (Sep 22, 2023)
5-139680734-A-G		not specified	Uncertain significance (Dec 22, 2023)
5-139680782-A-G		not specified	Likely benign (Feb 09, 2025)
5-139680788-G-A		not specified	Uncertain significance (Feb 17, 2024)
5-139680818-G-A		not specified	Uncertain significance (Dec 01, 2022)
5-139680821-G-A		not specified	Uncertain significance (Jan 21, 2025)
5-139680825-C-G		not specified	Uncertain significance (Jan 23, 2025)
5-139680854-G-A		not specified	Uncertain significance (Jun 07, 2024)
5-139680891-C-T		not specified	Uncertain significance (May 07, 2024)
5-139680900-C-T		not specified	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXXC5	protein_coding	protein_coding	ENST00000302517	2	36584

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	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	157	223	0.703	0.0000155	2102
Missense in Polyphen		34	73.653	0.46162		678
Synonymous	0.607	90	97.6	0.922	0.00000773	682
Loss of Function	2.47	0	7.13	0.00	3.70e-7	85

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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May indirectly participate in activation of the NF- kappa-B and MAPK pathways. Acts as a mediator of BMP4-mediated modulation of canonical Wnt signaling activity in neural stem cells (By similarity). Required for DNA damage-induced ATM phosphorylation, p53 activation and cell cycle arrest. Involved in myelopoiesis. Transcription factor. Binds to the oxygen responsive element of COX4I2 and represses its transcription under hypoxia conditions (4% oxygen), as well as normoxia conditions (20% oxygen) (PubMed:23303788). May repress COX4I2 transactivation induced by CHCHD2 and RBPJ (PubMed:23303788). {ECO:0000250, ECO:0000269|PubMed:19182210, ECO:0000269|PubMed:19557330, ECO:0000269|PubMed:23303788}.
• Pathway: Signal Transduction;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;ESR-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.441
• hipred: Y
• hipred_score: 0.593
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.927

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cxxc5
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; cellular phenotype; craniofacial phenotype

Zebrafish Information Network

• Gene name: cxxc5a
• Affected structure: caudal vein plexus
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of I-kappaB kinase/NF-kappaB signaling
• Cellular component: nucleoplasm;cytosol
• Molecular function: protein binding;transcription factor binding;zinc ion binding;sequence-specific DNA binding