ZNF540

zinc finger protein 540, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:37551405-37614179

Links

ENSG00000171817 ∙ NCBI:163255 ∙ OMIM:613903 ∙ HGNC:25331 ∙ Uniprot:Q8NDQ6 ∙ 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 ZNF540 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF540 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	3		36
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	3	0

Variants in ZNF540

This is a list of pathogenic ClinVar variants found in the ZNF540 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-37564620-T-G		not specified	Uncertain significance (Nov 09, 2022)
19-37564658-C-G		not specified	Uncertain significance (Sep 06, 2022)
19-37564675-G-A		not specified	Uncertain significance (Aug 12, 2022)
19-37564722-C-T		not specified	Uncertain significance (Nov 16, 2022)
19-37564726-T-C		not specified	Uncertain significance (Jun 22, 2021)
19-37564753-C-G		not specified	Uncertain significance (Nov 15, 2021)
19-37564779-C-T		not specified	Uncertain significance (Oct 26, 2021)
19-37564807-G-A		not specified	Uncertain significance (Mar 20, 2024)
19-37564867-G-T		not specified	Uncertain significance (Jan 04, 2022)
19-37564873-C-T		not specified	Uncertain significance (Feb 01, 2023)
19-37564974-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-37564989-C-A		not specified	Uncertain significance (Sep 14, 2022)
19-37565002-A-G		not specified	Uncertain significance (Dec 19, 2022)
19-37565034-T-G		not specified	Uncertain significance (Jul 11, 2023)
19-37565056-G-A		not specified	Uncertain significance (Sep 21, 2023)
19-37565194-T-C		not specified	Uncertain significance (Oct 18, 2021)
19-37565225-A-C		not specified	Uncertain significance (Jan 24, 2024)
19-37565256-T-C		not specified	Uncertain significance (Sep 20, 2023)
19-37565268-C-G		not specified	Uncertain significance (Dec 06, 2021)
19-37565308-G-A		not specified	Uncertain significance (May 04, 2022)
19-37565311-A-G		not specified	Uncertain significance (Dec 28, 2022)
19-37565313-A-C		not specified	Uncertain significance (Dec 13, 2021)
19-37565323-C-T		not specified	Uncertain significance (Feb 09, 2023)
19-37565412-T-C		not specified	Uncertain significance (Jul 05, 2023)
19-37565472-C-T			Benign (Aug 03, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF540	protein_coding	protein_coding	ENST00000592533	4	62691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.390	0.572	125627	0	1	125628	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.659	316	351	0.901	0.0000180	4398
Missense in Polyphen		100	114.96	0.86987		1464
Synonymous	0.781	107	118	0.908	0.00000588	1147
Loss of Function	1.64	1	4.94	0.202	2.07e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a transcriptional repressor. {ECO:0000269|PubMed:16815308}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0835

Intolerance Scores

• loftool: 0.771
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.17

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.132
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0100

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;negative regulation of translation;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;intracellular membrane-bounded organelle
• Molecular function: translation repressor activity, mRNA regulatory element binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding