ZMAT5

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

Basic information

Region (hg38): 22:29730956-29767011

Previous symbols: [ "ZC3H19" ]

Links

ENSG00000100319 ∙ NCBI:55954 ∙ OMIM:619741 ∙ HGNC:28046 ∙ Uniprot:Q9UDW3 ∙ 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 ZMAT5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMAT5 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 ZMAT5

This is a list of pathogenic ClinVar variants found in the ZMAT5 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29731278-G-A		not specified	Uncertain significance (Apr 14, 2022)
22-29731314-C-A		not specified	Uncertain significance (Dec 06, 2022)
22-29740691-A-G		not specified	Uncertain significance (Nov 17, 2023)
22-29742444-C-T		not specified	Uncertain significance (Sep 15, 2021)
22-29742468-A-G		not specified	Uncertain significance (Dec 07, 2023)
22-29742469-T-C		not specified	Uncertain significance (Sep 27, 2022)
22-29748483-C-T		not specified	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMAT5	protein_coding	protein_coding	ENST00000397781	5	36056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000152	0.667	125695	0	52	125747	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.759	75	95.9	0.782	0.00000552	1082
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000268
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000874	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.000210	0.000202
Middle Eastern	0.000874	0.000870
South Asian	0.000101	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of RNA;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

• loftool: 0.567
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.394
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.892

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmat5

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA splicing
• Cellular component: nucleoplasm;U12-type spliceosomal complex
• Molecular function: zinc ion binding