ZNF143

zinc finger protein 143, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 11:9460318-9528524

Links

ENSG00000166478 ∙ NCBI:7702 ∙ OMIM:603433 ∙ HGNC:12928 ∙ Uniprot:P52747 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• methylmalonic aciduria and homocystinuria (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF143 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF143 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	28	2	31
missense			42	2	2	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	4	4	10
non coding				8	32	40
Total	0	0	43	38	36

Variants in ZNF143

This is a list of pathogenic ClinVar variants found in the ZNF143 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-9471331-G-A		not specified	Uncertain significance (Apr 24, 2023)
11-9471343-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-9471353-G-A			Likely benign (Dec 30, 2023)
11-9471377-G-T			Likely benign (Jan 28, 2023)
11-9471414-G-A		not specified	Uncertain significance (Dec 26, 2023)
11-9471551-G-GT			Benign (May 19, 2021)
11-9471553-G-T			Benign (May 16, 2021)
11-9471604-G-A			Benign (May 23, 2021)
11-9472489-T-A			Benign (Jun 01, 2021)
11-9472519-C-T			Benign (May 18, 2021)
11-9472662-A-G			Likely benign (Jun 15, 2023)
11-9472669-TG-T			Likely benign (Jun 10, 2022)
11-9472672-A-G			Likely benign (Jun 04, 2022)
11-9472673-A-G			Uncertain significance (Sep 18, 2021)
11-9472687-C-G			Uncertain significance (Oct 18, 2023)
11-9472698-T-C		not specified	Uncertain significance (Apr 09, 2023)
11-9472712-T-G			Uncertain significance (Jan 06, 2023)
11-9472714-G-T		not specified	Uncertain significance (Jan 04, 2022)
11-9472731-C-G		not specified	Uncertain significance (Mar 31, 2023)
11-9472755-A-G		not specified	Uncertain significance (Dec 22, 2023)
11-9472785-A-G			Benign (May 29, 2023)
11-9472914-C-CT			Benign (May 25, 2021)
11-9473937-A-C		ZNF143-related disorder	Likely benign (Jan 17, 2024)
11-9473943-G-A			Uncertain significance (Jan 23, 2024)
11-9474006-G-A			Uncertain significance (Nov 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF143	protein_coding	protein_coding	ENST00000396602	15	68206

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000244	1.00	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	254	359	0.708	0.0000183	4169
Missense in Polyphen		49	95.225	0.51457		1163
Synonymous	-1.16	152	135	1.13	0.00000792	1234
Loss of Function	3.30	12	32.2	0.372	0.00000149	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000250	0.000244
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000462	0.000457
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator. Activates the gene for selenocysteine tRNA (tRNAsec). Binds to the SPH motif of small nuclear RNA (snRNA) gene promoters. Participates in efficient U6 RNA polymerase III transcription via its interaction with CHD8. {ECO:0000269|PubMed:17938208, ECO:0000269|PubMed:9776743}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 3 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription (Consensus)

Recessive Scores

• pRec: 0.216

Intolerance Scores

• loftool: 0.486
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.556
• hipred: Y
• hipred_score: 0.515
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp143
• Phenotype: reproductive system phenotype

Zebrafish Information Network

• Gene name: znf143b
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase III;transcription by RNA polymerase II;transcription by RNA polymerase III;snRNA transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;metal ion binding