ZIM2

zinc finger imprinted 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:56774547-56840731

Links

ENSG00000269699 ∙ NCBI:23619 ∙ ∙ HGNC:12875 ∙ Uniprot:Q9NZV7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Schizophrenia	AD	General	Evidence or clinical applicability unclear	Neurologic	21743468

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZIM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZIM2 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			22	10	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		2	3
non coding			71	24	16	111
Total	0	0	93	34	17

Variants in ZIM2

This is a list of pathogenic ClinVar variants found in the ZIM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-56774699-C-T		not specified	Likely benign (Feb 17, 2024)
19-56774713-T-C		not specified	Uncertain significance (May 25, 2022)
19-56774762-C-T		not specified	Likely benign (Dec 12, 2023)
19-56774774-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-56774795-G-T		not specified	Uncertain significance (Dec 27, 2023)
19-56774905-C-T		not specified	Uncertain significance (Apr 20, 2024)
19-56774956-A-G		not specified	Likely benign (Jan 23, 2024)
19-56775008-G-A		not specified	Uncertain significance (Aug 02, 2021)
19-56775016-T-C		not specified	Likely benign (Oct 30, 2023)
19-56775019-C-T		not specified	Uncertain significance (May 25, 2022)
19-56775113-T-C		not specified	Uncertain significance (May 14, 2024)
19-56775115-C-A		not specified	Uncertain significance (Oct 25, 2023)
19-56775265-G-A		not specified	Uncertain significance (May 25, 2022)
19-56775291-G-T		not specified	Uncertain significance (Aug 17, 2022)
19-56775320-G-A		not specified	Uncertain significance (Jan 08, 2024)
19-56775414-A-T		not specified	Uncertain significance (Aug 14, 2023)
19-56775493-C-T		not specified	Uncertain significance (Jul 13, 2022)
19-56775517-T-C		not specified	Uncertain significance (Jan 11, 2023)
19-56775521-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-56779394-T-C		not specified	Uncertain significance (Sep 17, 2021)
19-56779398-T-C		not specified	Uncertain significance (Mar 07, 2024)
19-56781970-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-56781989-C-T		not specified	Uncertain significance (May 14, 2024)
19-56781995-T-A		not specified	Uncertain significance (Sep 16, 2021)
19-56782105-T-C		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZIM2	protein_coding	protein_coding	ENST00000391708	9	66178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00181	0.977	125737	0	7	125744	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.146	305	298	1.02	0.0000167	3507
Missense in Polyphen		40	45.293	0.88314		578
Synonymous	-0.488	116	110	1.06	0.00000639	952
Loss of Function	2.02	7	15.6	0.449	8.46e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.679
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.54

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.214

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II
• Cellular component: cellular_component;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;zinc ion binding