ZMAT1

protein-coding

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

Gene summary

This gene encodes a protein containing Cys2-His2 (C2H2)-type zinc fingers, which are similar to those found in the nuclear matrix protein matrin 3. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

MANE transcript

NM_001394560.1

Inheritance

—

ClinVar variants

U:95B:7

Top phenotype

Abnormality of neuronal migration

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chrX:101,882,288-101,932,031

External References & Databases

Ensembl (ENSG00000166432)

Transcript & Mutation Effects

hg38 • Region Span ~49.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZMAT1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 2

Abnormality of neuronal migrationTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394560.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	1 clinvar		7
missense			75 clinvar	5 clinvar	1 clinvar	81
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			11 clinvar			11
Total	0	0	95	6	1	102

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394560.1	RefSeq	NP_001381489.1	6	MANE Select
ENST00000651725.2	Ensembl	ENSP00000498446.1	6	MANE Select
NM_001011657.4	RefSeq	NP_001011657.2	6	Standard
NM_001282400.2	RefSeq	NP_001269329.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

DNA binding
zinc ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372782
Coding exons: 6
Length: 49743
Individuals with no LoFs: 125675
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125682
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.443	187	205	0.913	0.0000140	4256
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000076	0.000062	rare
Latino/Admixed American	0.000043	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000026	rare
South Asian	0.00011	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.537
RVIS EVS: 0.22
RVIS percentile EVS: 68.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.00965

Gene Damage Prediction

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