CXXC1

CXXC finger protein 1, the group of PHD finger proteins|Zinc fingers CXXC-type

Basic information

Region (hg38): 18:50282343-50287839

Links

ENSG00000154832 ∙ NCBI:30827 ∙ OMIM:609150 ∙ HGNC:24343 ∙ Uniprot:Q9P0U4 ∙ 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 CXXC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CXXC1 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				2	5	7
missense			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					2	2
Total	0	0	35	2	7

Variants in CXXC1

This is a list of pathogenic ClinVar variants found in the CXXC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-50282606-C-A		not specified	Uncertain significance (Jan 05, 2022)
18-50282632-A-T		not specified	Uncertain significance (Feb 21, 2024)
18-50283340-A-G			Benign (Dec 31, 2019)
18-50283514-C-G			Uncertain significance (Aug 07, 2018)
18-50283551-G-A		not specified	Uncertain significance (Apr 27, 2022)
18-50283563-T-A		not specified	Uncertain significance (Nov 09, 2024)
18-50283881-C-G			Benign (May 10, 2019)
18-50283907-C-T		not specified	Uncertain significance (Dec 20, 2024)
18-50283962-G-A		not specified	Uncertain significance (Feb 11, 2025)
18-50283977-G-C		not specified	Uncertain significance (Dec 02, 2021)
18-50283981-A-G			Benign (May 10, 2019)
18-50283992-T-C		not specified	Uncertain significance (Aug 21, 2023)
18-50284393-A-C		not specified	Uncertain significance (Nov 13, 2023)
18-50284433-C-T		not specified	Uncertain significance (Nov 08, 2024)
18-50284441-A-G		not specified	Uncertain significance (Jan 03, 2024)
18-50284541-G-A		not specified	Uncertain significance (Dec 19, 2023)
18-50284558-T-G		not specified	Uncertain significance (Oct 22, 2024)
18-50284797-C-T		not specified	Uncertain significance (Jan 08, 2024)
18-50285013-C-A		not specified	Uncertain significance (Oct 25, 2022)
18-50285061-G-A		not specified	Uncertain significance (Jul 10, 2024)
18-50285094-C-T		not specified	Uncertain significance (Sep 27, 2024)
18-50285111-T-G		not specified	Uncertain significance (Dec 28, 2023)
18-50285141-T-G		not specified	Uncertain significance (Aug 20, 2024)
18-50285204-C-T		not specified	Uncertain significance (Jan 03, 2025)
18-50285205-G-A		not specified	Uncertain significance (Apr 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CXXC1	protein_coding	protein_coding	ENST00000412036	15	5962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.895	0.105	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.15	256	442	0.579	0.0000325	4289
Missense in Polyphen		73	217	0.3364		2161
Synonymous	-1.14	182	163	1.11	0.0000102	1274
Loss of Function	4.67	7	38.1	0.183	0.00000201	433

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000361	0.0000352
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator that exhibits a unique DNA binding specificity for CpG unmethylated motifs with a preference for CpGG. {ECO:0000269|PubMed:21407193}.
• Pathway: XBP1(S) activates chaperone genes (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.286
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.47

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.704
• ghis: 0.653

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cxxc1
• Phenotype: reproductive system 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); embryo phenotype

Zebrafish Information Network

• Gene name: cxxc1b
• Affected structure: blood vasculature
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;IRE1-mediated unfolded protein response;positive regulation of transcription, DNA-templated;histone H3-K4 methylation
• Cellular component: nucleus;nucleoplasm;cytosol;nuclear matrix;nuclear speck;histone methyltransferase complex;Set1C/COMPASS complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;protein binding;zinc ion binding;histone methyltransferase activity (H3-K4 specific);unmethylated CpG binding