ZMAT2

zinc finger matrin-type 2, the group of Spliceosomal B complex|Zinc fingers matrin-type

Basic information

Region (hg38): 5:140698680-140706686

Links

ENSG00000146007

∙ NCBI:153527 ∙ OMIM:619930 ∙ HGNC:26433 ∙ Uniprot:Q96NC0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

congenital radioulnar synostosis (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMAT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMAT2 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			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in ZMAT2

This is a list of pathogenic ClinVar variants found in the ZMAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140703952-G-A		not specified	Uncertain significance (May 23, 2023)	2549685

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMAT2	protein_coding	protein_coding	ENST00000274712	6	7984

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0158	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	34	112	0.303	0.00000587	1341
Missense in Polyphen		5	24.719	0.20227		282
Synonymous	0.0123	37	37.1	0.997	0.00000182	319
Loss of Function	3.29	0	12.6	0.00	7.16e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in pre-mRNA splicing as a component of the spliceosome. {ECO:0000269|PubMed:28781166}.;
Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool
rvis_EVS: -0.03
rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

pHI: 0.642
hipred: Y
hipred_score: 0.673
ghis: 0.583

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Zmat2
Phenotype

Zebrafish Information Network

Gene name: zmat2
Affected structure: head
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: mRNA splicing, via spliceosome
Cellular component: nucleus;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome
Molecular function: DNA binding;protein binding;zinc ion binding