ZMAT5

protein-coding

zinc finger matrin-type 5, the group of U11/U12 di-snRNP|Zinc fingers CCCH-type|Zinc fingers matrin-type

Gene summary

Predicted to enable zinc ion binding activity. Predicted to be involved in spliceosome conformational change to release U4 (or U4atac) and U1 (or U11). Located in nucleoplasm. Part of U12-type spliceosomal complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZC3H19

MANE transcript

NM_001003692.2

Inheritance

—

ClinVar variants

U:25

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr22:29,730,956-29,767,011

External References & Databases

Ensembl (ENSG00000100319)

Transcript & Mutation Effects

hg38 • Region Span ~36.1 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 ZMAT5 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001003692.2. 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						0
missense			23 clinvar			23
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	25	0	0	25

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 64 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001003692.2	RefSeq	NP_001003692.1	5	MANE Select
ENST00000344318.4	Ensembl	ENSP00000344241.3	5	MANE Select
NM_001318129.2	RefSeq	NP_001305058.1	5	Standard
NM_019103.3	RefSeq	NP_061976.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of RNA
mRNA Splicing - Minor Pathway
mRNA Splicing
Processing of Capped Intron-Containing Pre-mRNA

Biological Process

mRNA splicing, via spliceosome
RNA splicing

Molecular Function

zinc ion binding

Cellular Component

nucleoplasm
U12-type spliceosomal complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397781
Coding exons: 5
Length: 36056
Individuals with no LoFs: 125695
Homozygous LoFs: 0
Heterozygous LoFs: 52
Defined: 125747
p: 0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.759	75	95.9	0.782	0.00000552	1082
Missense (PolyPhen)		20	32.324	0.61873		372
Synonymous	0.539	35	39.3	0.891	0.00000225	324
Loss of Function	0.954	9	12.7	0.711	8.81e-7	105

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00087	0.00087	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00020	rare
South Asian	0.00010	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.567
RVIS EVS: 0.13
RVIS percentile EVS: 62.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.892

Gene Damage Prediction

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