ZMAT1

zinc finger matrin-type 1, the group of Zinc fingers matrin-type

Basic information

Region (hg38): X:101882288-101932031

Links

ENSG00000166432 ∙ NCBI:84460 ∙ OMIM:301007 ∙ HGNC:29377 ∙ Uniprot:Q5H9K5 ∙ 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 ZMAT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMAT1 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	0

Variants in ZMAT1

This is a list of pathogenic ClinVar variants found in the ZMAT1 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-101883608-C-T		not specified	Uncertain significance (Apr 06, 2023)
X-101883614-G-A		Abnormality of neuronal migration	Benign (Oct 31, 2014)
X-101883631-T-C		not specified	Uncertain significance (Oct 06, 2021)
X-101883632-T-C		not specified	Uncertain significance (Oct 12, 2021)
X-101883715-T-A			Likely benign (Apr 01, 2023)
X-101883723-T-C			Likely benign (Nov 01, 2022)
X-101883821-G-A		not specified	Uncertain significance (Sep 20, 2023)
X-101883920-G-T		not specified	Uncertain significance (Aug 08, 2022)
X-101883998-G-C		not specified	Uncertain significance (May 31, 2023)
X-101884039-T-C		not specified	Uncertain significance (Jan 31, 2022)
X-101884110-C-G		not specified	Uncertain significance (Jun 19, 2024)
X-101884118-G-A		not specified	Uncertain significance (Dec 12, 2023)
X-101884261-T-G		not specified	Uncertain significance (Feb 12, 2024)
X-101884316-A-G		not specified	Uncertain significance (Jul 19, 2023)
X-101884393-G-C		not specified	Uncertain significance (Nov 03, 2023)
X-101884418-G-T		not specified	Uncertain significance (Jun 17, 2024)
X-101884523-C-A		not specified	Uncertain significance (Jul 07, 2022)
X-101884595-G-A		not specified	Likely benign (Aug 26, 2022)
X-101886650-C-T		not specified	Uncertain significance (Sep 17, 2021)
X-101886725-C-A		not specified	Uncertain significance (Jun 30, 2023)
X-101898139-T-C		not specified	Uncertain significance (Feb 21, 2024)
X-101898208-C-A		not specified	Uncertain significance (Jan 31, 2024)
X-101904327-G-A		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMAT1	protein_coding	protein_coding	ENST00000372782	6	49743

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00105	0.989	125675	0	7	125682	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.443	187	205	0.913	0.0000140	4256
Missense in Polyphen		18	31.94	0.56356		767
Synonymous	0.535	62	67.6	0.917	0.00000454	1085
Loss of Function	2.26	8	18.5	0.432	0.00000139	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000104
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000371	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000109	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.537
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.154
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmat1

Gene ontology

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