ZMAT3

zinc finger matrin-type 3, the group of Zinc fingers matrin-type

Basic information

Region (hg38): 3:178960120-179072215

Links

ENSG00000172667 ∙ NCBI:64393 ∙ OMIM:606452 ∙ HGNC:29983 ∙ Uniprot:Q9HA38 ∙ 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 ZMAT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMAT3 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in ZMAT3

This is a list of pathogenic ClinVar variants found in the ZMAT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-179025045-T-C		not specified	Likely benign (Jan 05, 2022)
3-179025054-C-T		not specified	Uncertain significance (Jul 26, 2021)
3-179025055-G-A		not specified	Uncertain significance (Jun 29, 2023)
3-179025072-C-T		not specified	Uncertain significance (Jul 05, 2023)
3-179025202-G-A		not specified	Uncertain significance (Nov 12, 2021)
3-179027464-A-T		not specified	Uncertain significance (Aug 23, 2021)
3-179027477-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-179027772-G-A		not specified	Uncertain significance (Apr 05, 2023)
3-179030884-G-A		not specified	Uncertain significance (Jan 05, 2022)
3-179030965-T-C		not specified	Uncertain significance (Apr 05, 2023)
3-179067524-C-T		not specified	Uncertain significance (Dec 22, 2023)
3-179067545-G-T		not specified	Uncertain significance (Aug 02, 2021)
3-179067559-T-G		not specified	Uncertain significance (Nov 06, 2023)
3-179067571-C-T		Malignant tumor of prostate	Uncertain significance (-)
3-179067572-A-T		not specified	Likely benign (Nov 18, 2022)
3-179067641-G-C		not specified	Uncertain significance (Jun 01, 2023)
3-179067731-C-T		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMAT3	protein_coding	protein_coding	ENST00000311417	5	55057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000190	0.907	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.778	138	166	0.830	0.00000947	1877
Missense in Polyphen		43	63.592	0.67619		701
Synonymous	1.06	52	62.7	0.830	0.00000346	571
Loss of Function	1.52	8	14.2	0.564	8.44e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a bona fide target gene of p53/TP53. May play a role in the TP53-dependent growth regulatory pathway. May contribute to TP53-mediated apoptosis by regulation of TP53 expression and translocation to the nucleus and nucleolus. {ECO:0000269|PubMed:11571644}.
• Pathway: p53 signaling pathway - Homo sapiens (human);miRNA regulation of p53 pathway in prostate cancer (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.732
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.369
• ghis: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmat3

Gene ontology

• Biological process: apoptotic process;cellular response to DNA damage stimulus;protein transport;regulation of growth;positive regulation of apoptotic process
• Cellular component: nucleoplasm;nucleolus;plasma membrane
• Molecular function: RNA binding;protein binding;zinc ion binding