ZNF587B

zinc finger protein 587B, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57819721-57846238

Links

ENSG00000269343 ∙ NCBI:100293516 ∙ ∙ HGNC:37142 ∙ Uniprot:E7ETH6 ∙ 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 ZNF587B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF587B 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			23	1	2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	2

Variants in ZNF587B

This is a list of pathogenic ClinVar variants found in the ZNF587B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57830533-C-T		not specified	Uncertain significance (Jan 19, 2024)
19-57830563-A-G		not specified	Uncertain significance (Sep 27, 2021)
19-57839036-T-C		not specified	Uncertain significance (Aug 08, 2022)
19-57839055-A-C		not specified	Likely benign (Aug 08, 2022)
19-57839075-A-G		not specified	Uncertain significance (Nov 14, 2023)
19-57839084-G-A			Benign (Feb 09, 2018)
19-57839105-A-G		not specified	Uncertain significance (May 31, 2023)
19-57839108-G-A		not specified	Uncertain significance (Jun 04, 2024)
19-57840858-G-T		not specified	Uncertain significance (Mar 11, 2024)
19-57840915-A-T		not specified	Uncertain significance (Mar 01, 2024)
19-57840970-C-T		not specified	Uncertain significance (Jul 08, 2022)
19-57841014-C-T		not specified	Uncertain significance (May 13, 2024)
19-57841101-A-G		not specified	Uncertain significance (Oct 05, 2023)
19-57841126-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-57841218-A-G		not specified	Uncertain significance (May 09, 2022)
19-57841229-A-T		not specified	Uncertain significance (Apr 12, 2022)
19-57841320-C-T		not specified	Uncertain significance (Mar 31, 2024)
19-57841321-A-G		not specified	Uncertain significance (Mar 31, 2024)
19-57841328-T-A		not specified	Likely benign (Mar 31, 2024)
19-57841378-T-A		not specified	Uncertain significance (Sep 01, 2021)
19-57841386-C-G			Benign (Feb 09, 2018)
19-57841387-G-A		not specified	Uncertain significance (Mar 17, 2023)
19-57841410-G-C		not specified	Uncertain significance (Jun 11, 2024)
19-57841413-T-A		not specified	Uncertain significance (Dec 19, 2023)
19-57841423-C-A		not specified	Uncertain significance (Dec 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF587B	protein_coding	protein_coding	ENST00000442832	4	38920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.80e-13	0.00655	125177	0	2	125179	0.00000799

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.454	219	201	1.09	0.00000996	2637
Missense in Polyphen		55	55.155	0.99718		758
Synonymous	-1.79	90	70.8	1.27	0.00000361	697
Loss of Function	-0.885	17	13.5	1.26	6.27e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000124
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 be involved in transcriptional regulation. {ECO:0000305}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

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 by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;nucleic acid binding;metal ion binding