ZNF12

zinc finger protein 12, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 7:6688433-6706947

Previous symbols: [ "ZNF325" ]

Links

ENSG00000164631 ∙ NCBI:7559 ∙ OMIM:194536 ∙ HGNC:12902 ∙ Uniprot:P17014 ∙ 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 ZNF12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF12 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				1		1
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	0

Variants in ZNF12

This is a list of pathogenic ClinVar variants found in the ZNF12 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-6690856-G-A		not specified	Uncertain significance (Dec 31, 2023)
7-6690918-G-A		not specified	Uncertain significance (Mar 28, 2023)
7-6690990-T-C		not specified	Uncertain significance (Jul 25, 2024)
7-6691034-A-C		not specified	Uncertain significance (Aug 15, 2023)
7-6691111-C-G		not specified	Uncertain significance (Oct 17, 2024)
7-6691285-T-C		not specified	Uncertain significance (Jul 25, 2024)
7-6691401-G-A		not specified	Uncertain significance (Jul 09, 2024)
7-6691414-T-C		not specified	Uncertain significance (Oct 12, 2021)
7-6691462-C-T		not specified	Uncertain significance (Oct 01, 2024)
7-6691544-T-G		not specified	Uncertain significance (Dec 22, 2023)
7-6691659-A-C		not specified	Uncertain significance (Oct 06, 2023)
7-6691668-G-A		not specified	Uncertain significance (May 14, 2024)
7-6691694-T-G		not specified	Uncertain significance (Oct 11, 2021)
7-6691737-A-G		not specified	Uncertain significance (Aug 21, 2024)
7-6691791-T-C		not specified	Uncertain significance (Feb 28, 2023)
7-6691983-G-T		not specified	Uncertain significance (Jul 27, 2024)
7-6691992-C-T		not specified	Uncertain significance (Oct 13, 2023)
7-6692021-G-A			Likely benign (Mar 01, 2023)
7-6692050-C-T		not specified	Uncertain significance (Dec 20, 2021)
7-6692154-T-C		not specified	Uncertain significance (Oct 04, 2022)
7-6692166-T-G		not specified	Uncertain significance (Mar 22, 2023)
7-6692181-G-A		not specified	Uncertain significance (Aug 14, 2023)
7-6692220-T-C		not specified	Uncertain significance (Feb 28, 2024)
7-6692274-T-A		not specified	Uncertain significance (Nov 20, 2024)
7-6692278-A-G		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF12	protein_coding	protein_coding	ENST00000405858	4	18491

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0397	0.960	125726	0	21	125747	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	284	364	0.781	0.0000174	4615
Missense in Polyphen		119	193.66	0.61448		2393
Synonymous	-2.18	160	129	1.24	0.00000658	1206
Loss of Function	3.54	8	28.3	0.283	0.00000132	428

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor which suppresses activation protein 1 (AP-1)- and serum response element (SRE)-mediated transcriptional activity. {ECO:0000269|PubMed:16806083}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.542
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.427
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.623

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp12

Gene ontology

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