ZXDA

zinc finger X-linked duplicated A, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): X:57905430-57910458

Links

ENSG00000198205 ∙ NCBI:7789 ∙ OMIM:300235 ∙ HGNC:13198 ∙ Uniprot:P98168 ∙ 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 ZXDA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZXDA 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				4		4
missense			40	7		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	11	0

Variants in ZXDA

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

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

Position	Type	Phenotype	Significance	ClinVar
X-57908055-A-T		not specified	Uncertain significance (Jan 20, 2025)
X-57908059-T-A		not specified	Uncertain significance (May 23, 2023)
X-57908152-C-T		not specified	Uncertain significance (Apr 12, 2024)
X-57908154-C-T		not specified	Likely benign (Apr 01, 2023)
X-57908170-C-T		not specified	Likely benign (Apr 01, 2023)
X-57908227-T-C		not specified	Likely benign (Feb 11, 2022)
X-57908271-G-A		not specified	Uncertain significance (Nov 09, 2024)
X-57908304-T-C		not specified	Likely benign (Mar 20, 2024)
X-57908377-T-G		not specified	Uncertain significance (Oct 16, 2023)
X-57908467-C-T		not specified	Uncertain significance (Dec 28, 2024)
X-57908493-T-C		not specified	Uncertain significance (Feb 08, 2025)
X-57908593-C-T		not specified	Uncertain significance (Nov 15, 2024)
X-57908673-G-T		not specified	Uncertain significance (Apr 22, 2022)
X-57908701-G-T		not specified	Uncertain significance (Jan 16, 2024)
X-57908706-T-A		not specified	Uncertain significance (Jul 07, 2024)
X-57908784-G-A		not specified	Uncertain significance (Feb 05, 2025)
X-57908803-T-G		not specified	Uncertain significance (Jan 30, 2024)
X-57908806-C-T		not specified	Uncertain significance (Feb 11, 2025)
X-57908874-C-T		not specified	Uncertain significance (Feb 05, 2025)
X-57908890-C-A		not specified	Uncertain significance (Nov 23, 2024)
X-57908890-C-T		not specified	Uncertain significance (Jan 14, 2025)
X-57908954-T-G		not specified	Uncertain significance (Apr 28, 2023)
X-57908988-C-T		not specified	Uncertain significance (Sep 03, 2024)
X-57909040-A-C		not specified	Uncertain significance (Nov 21, 2024)
X-57909210-C-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZXDA	protein_coding	protein_coding	ENST00000358697	1	5204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00437	0.880	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.193	289	298	0.969	0.0000245	5154
Missense in Polyphen		127	149.15	0.8515		2648
Synonymous	-0.659	154	144	1.07	0.0000133	1703
Loss of Function	1.33	5	9.41	0.531	5.99e-7	189

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: Cooperates with CIITA to promote transcription of MHC class I and MHC class II genes. {ECO:0000269|PubMed:17493635}.

Recessive Scores

• pRec: 0.0978

Haploinsufficiency Scores

• pHI: 0.196
• hipred: N
• hipred_score: 0.187
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zxdb

Gene ontology

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