ZIM3

zinc finger imprinted 3, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57134096-57145202

Links

ENSG00000141946 ∙ NCBI:114026 ∙ ∙ HGNC:16366 ∙ Uniprot:Q96PE6 ∙ 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 ZIM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZIM3 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in ZIM3

This is a list of pathogenic ClinVar variants found in the ZIM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57134934-C-A		not specified	Uncertain significance (Oct 26, 2021)
19-57134965-C-G		not specified	Uncertain significance (Apr 13, 2022)
19-57134974-C-G		not specified	Uncertain significance (Jan 31, 2022)
19-57134974-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-57134980-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-57134991-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-57135012-G-T		not specified	Uncertain significance (Jun 18, 2021)
19-57135016-G-A		not specified	Uncertain significance (Mar 02, 2023)
19-57135093-C-G		not specified	Uncertain significance (Jul 20, 2021)
19-57135291-T-C		not specified	Uncertain significance (Jun 18, 2021)
19-57135325-T-C		not specified	Uncertain significance (May 20, 2024)
19-57135346-C-T		not specified	Uncertain significance (Feb 06, 2024)
19-57135348-G-A		not specified	Uncertain significance (Sep 17, 2021)
19-57135358-T-C		not specified	Uncertain significance (Oct 06, 2022)
19-57135360-T-C		not specified	Uncertain significance (Sep 22, 2023)
19-57135366-T-G		not specified	Uncertain significance (Jan 23, 2024)
19-57135393-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-57135393-G-C		not specified	Uncertain significance (Dec 27, 2022)
19-57135397-T-C		not specified	Uncertain significance (Sep 22, 2022)
19-57135412-A-G		not specified	Uncertain significance (Jul 20, 2021)
19-57135527-C-G		not specified	Uncertain significance (Nov 21, 2022)
19-57135586-A-G		not specified	Uncertain significance (Jun 10, 2022)
19-57135622-A-G		not specified	Likely benign (Apr 25, 2022)
19-57135687-T-C		not specified	Uncertain significance (Aug 09, 2021)
19-57135688-G-C		not specified	Uncertain significance (Apr 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZIM3	protein_coding	protein_coding	ENST00000269834	4	11107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000179	0.463	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.520	264	241	1.09	0.0000125	3151
Missense in Polyphen		67	67.883	0.98699		899
Synonymous	-0.640	100	92.2	1.08	0.00000540	803
Loss of Function	0.495	8	9.66	0.828	4.14e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.000217	0.000217
South Asian	0.000359	0.000359
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: 0.0797

Intolerance Scores

• loftool: 0.893
• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.97

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0756

Gene Damage Prediction

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

Gene ontology

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