ZXDC

ZXD family zinc finger C, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:126437601-126475891

Links

ENSG00000070476 ∙ NCBI:79364 ∙ OMIM:615746 ∙ HGNC:28160 ∙ Uniprot:Q2QGD7 ∙ 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 ZXDC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZXDC 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			70	3		73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	70	3	0

Variants in ZXDC

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

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

Position	Type	Phenotype	Significance	ClinVar
3-126438436-G-C		not specified	Uncertain significance (Jan 26, 2022)
3-126439646-C-T		not specified	Uncertain significance (Oct 02, 2023)
3-126439653-G-T		not specified	Uncertain significance (Apr 22, 2022)
3-126439712-C-T		not specified	Uncertain significance (Jan 31, 2024)
3-126441785-C-T		not specified	Uncertain significance (Dec 13, 2022)
3-126441790-T-C		not specified	Uncertain significance (Jun 07, 2024)
3-126441802-T-C		not specified	Uncertain significance (Apr 05, 2023)
3-126441814-G-T		not specified	Uncertain significance (Aug 17, 2021)
3-126441845-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-126441859-C-T		not specified	Uncertain significance (Nov 21, 2023)
3-126441862-C-T		not specified	Uncertain significance (May 24, 2023)
3-126441886-T-C		not specified	Uncertain significance (Sep 19, 2022)
3-126441887-G-T		not specified	Uncertain significance (Oct 26, 2022)
3-126441912-T-A		not specified	Uncertain significance (Sep 20, 2023)
3-126459671-C-T		not specified	Uncertain significance (Oct 12, 2022)
3-126461614-T-C		not specified	Likely benign (Jul 13, 2021)
3-126461638-T-C		not specified	Uncertain significance (Feb 26, 2024)
3-126461674-G-A		not specified	Uncertain significance (Sep 29, 2023)
3-126461705-G-A		not specified	Uncertain significance (Nov 14, 2023)
3-126461713-G-C		not specified	Uncertain significance (Aug 02, 2021)
3-126461715-A-C		not specified	Uncertain significance (Aug 04, 2023)
3-126461725-G-C		not specified	Uncertain significance (Apr 23, 2024)
3-126461728-G-A		not specified	Uncertain significance (Jun 29, 2023)
3-126461744-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-126461773-T-C		not specified	Likely benign (Aug 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZXDC	protein_coding	protein_coding	ENST00000389709	10	38319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-9	0.773	125530	0	31	125561	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	357	438	0.815	0.0000239	5473
Missense in Polyphen		111	182.68	0.60762		2107
Synonymous	-1.04	206	188	1.10	0.0000112	1837
Loss of Function	1.54	18	26.6	0.678	0.00000136	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000309	0.000303
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000980
Other	0.000332	0.000327

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cooperates with CIITA to promote transcription of MHC class I and MHC class II genes. {ECO:0000269|PubMed:16600381, ECO:0000269|PubMed:17493635, ECO:0000269|PubMed:17696781}.

Intolerance Scores

• loftool: 0.679
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.73

Haploinsufficiency Scores

• pHI: 0.0784
• hipred: N
• hipred_score: 0.330
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.718

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zxdc

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;positive regulation of transcription, DNA-templated
• Cellular component: cellular_component;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;nucleic acid binding;DNA-binding transcription factor activity;protein binding;LRR domain binding;metal ion binding;C2H2 zinc finger domain binding