ZNF154

zinc finger protein 154, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57696275-57709204

Links

ENSG00000179909 ∙ NCBI:7710 ∙ OMIM:604085 ∙ HGNC:12939 ∙ Uniprot:Q13106 ∙ 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 ZNF154 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF154 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			26	1		27
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	1	0

Variants in ZNF154

This is a list of pathogenic ClinVar variants found in the ZNF154 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57701687-G-A		not specified	Uncertain significance (Nov 08, 2022)
19-57701717-T-C		not specified	Likely benign (Nov 12, 2021)
19-57701788-G-C		not specified	Uncertain significance (Jul 09, 2021)
19-57701894-G-T		not specified	Uncertain significance (Jan 08, 2024)
19-57701906-C-T		not specified	Uncertain significance (Jun 29, 2022)
19-57701907-G-A		not specified	Uncertain significance (Jun 29, 2022)
19-57701963-T-C		not specified	Uncertain significance (May 10, 2024)
19-57701970-T-C		not specified	Uncertain significance (Dec 16, 2023)
19-57701998-A-C		not specified	Uncertain significance (May 09, 2024)
19-57702000-T-A		not specified	Uncertain significance (May 09, 2024)
19-57702042-A-C		not specified	Uncertain significance (Apr 15, 2024)
19-57702045-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-57702116-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-57702185-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-57702204-C-G		not specified	Uncertain significance (Aug 16, 2022)
19-57702207-T-C		not specified	Uncertain significance (Aug 13, 2021)
19-57702236-A-C		not specified	Uncertain significance (Jan 03, 2024)
19-57702242-C-T		not specified	Uncertain significance (Jun 04, 2024)
19-57702377-C-T		not specified	Uncertain significance (Oct 17, 2023)
19-57702534-T-C		not specified	Uncertain significance (Aug 01, 2022)
19-57702567-T-C		not specified	Uncertain significance (Sep 25, 2023)
19-57702585-C-T		not specified	Uncertain significance (Jun 09, 2022)
19-57702644-A-G		not specified	Uncertain significance (Jun 29, 2023)
19-57702650-G-T		not specified	Uncertain significance (Apr 27, 2024)
19-57702710-C-T		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF154	protein_coding	protein_coding	ENST00000512439	3	11845

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.82e-7	0.525	122970	11	2667	125648	0.0107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.249	239	228	1.05	0.0000120	2911
Missense in Polyphen		90	82.097	1.0963		1119
Synonymous	-0.692	91	83.0	1.10	0.00000432	796
Loss of Function	0.899	12	15.9	0.757	9.38e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00579	0.00572
Ashkenazi Jewish	0.0146	0.0147
East Asian	0.00232	0.00229
Finnish	0.0164	0.0163
European (Non-Finnish)	0.0133	0.0134
Middle Eastern	0.00232	0.00229
South Asian	0.0135	0.0134
Other	0.0102	0.0102

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.597
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.99

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.112
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0213

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