ZMAT4

zinc finger matrin-type 4, the group of Zinc fingers matrin-type

Basic information

Region (hg38): 8:40530589-40897833

Links

ENSG00000165061 ∙ NCBI:79698 ∙ ∙ HGNC:25844 ∙ Uniprot:Q9H898 ∙ 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 ZMAT4 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMAT4 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in ZMAT4

This is a list of pathogenic ClinVar variants found in the ZMAT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-40581259-G-C		not specified	Uncertain significance (Nov 10, 2021)
8-40674814-T-G		not specified	Uncertain significance (Aug 15, 2023)
8-40674858-T-A		not specified	Uncertain significance (Feb 23, 2023)
8-40674905-G-A		not specified	Uncertain significance (Oct 06, 2021)
8-40697278-A-T		not specified	Uncertain significance (Apr 22, 2022)
8-40697397-C-A		not specified	Uncertain significance (Apr 12, 2022)
8-40767648-G-A		not specified	Uncertain significance (Jun 28, 2022)
8-40767693-A-G		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMAT4	protein_coding	protein_coding	ENST00000297737	6	367244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0755	0.914	125714	0	12	125726	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	83	126	0.657	0.00000689	1479
Missense in Polyphen		28	63.321	0.44219		761
Synonymous	-0.515	56	51.3	1.09	0.00000307	426
Loss of Function	2.23	4	12.5	0.319	6.70e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.527
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.543
• hipred: Y
• hipred_score: 0.546
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmat4

Gene ontology

• Cellular component: nucleus
• Molecular function: DNA binding;protein binding;zinc ion binding