ZNF875

zinc finger protein 875, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:37312836-37369365

Previous symbols: [ "HKR1" ]

Links

ENSG00000181666 ∙ NCBI:284459 ∙ OMIM:165250 ∙ HGNC:4928 ∙ Uniprot:P10072 ∙ 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 ZNF875 gene.

• Inborn genetic diseases (13 variants)
• not provided (7 variants)
• Arthrogryposis multiplex congenita;Fetal akinesia deformation sequence 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF875 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				5	1	6
missense			13		1	14
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	5	2

Variants in ZNF875

This is a list of pathogenic ClinVar variants found in the ZNF875 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-37344749-G-A		not specified	Uncertain significance (Apr 25, 2023)
19-37344773-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-37347191-C-T		not specified	Uncertain significance (Jan 06, 2023)
19-37347220-T-G			Benign (Jan 08, 2018)
19-37347309-C-T			Benign (Jan 08, 2018)
19-37347794-C-G		not specified	Uncertain significance (Oct 05, 2021)
19-37359637-T-G			Likely benign (Nov 01, 2023)
19-37359643-C-T			Likely benign (Nov 01, 2023)
19-37359649-G-A			Likely benign (Nov 01, 2023)
19-37359682-A-G			Likely benign (Mar 01, 2023)
19-37362132-A-T		not specified	Likely benign (Sep 29, 2022)
19-37362202-C-G		not specified	Uncertain significance (Mar 28, 2023)
19-37362211-T-G		not specified	Uncertain significance (Sep 27, 2022)
19-37362235-C-G		not specified	Uncertain significance (Nov 21, 2022)
19-37362283-A-T		not specified	Uncertain significance (Nov 14, 2023)
19-37362347-T-G		not specified	Uncertain significance (Nov 02, 2023)
19-37362354-G-A		not specified	Uncertain significance (Oct 25, 2023)
19-37362381-C-T		not specified	Likely benign (Sep 15, 2021)
19-37362684-G-A		not specified	Uncertain significance (May 18, 2023)
19-37362703-G-T		not specified	Uncertain significance (Dec 01, 2022)
19-37362763-A-G		not specified	Uncertain significance (Jan 18, 2023)
19-37362841-G-A		not specified	Uncertain significance (Jul 19, 2023)
19-37362933-A-G		not specified	Uncertain significance (Sep 13, 2023)
19-37362969-C-T		not specified	Uncertain significance (May 05, 2022)
19-37362978-C-T		not specified	Uncertain significance (Nov 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF875	protein_coding	protein_coding	ENST00000324411	4	56529

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.69e-19	0.00161	125111	0	636	125747	0.00253

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.349	378	359	1.05	0.0000187	4318
Missense in Polyphen		96	84.888	1.1309		1145
Synonymous	-1.10	150	134	1.12	0.00000665	1262
Loss of Function	-0.244	28	26.6	1.05	0.00000150	317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00307	0.00307
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00153	0.00152
Finnish	0.00605	0.00607
European (Non-Finnish)	0.00304	0.00303
Middle Eastern	0.00153	0.00152
South Asian	0.00138	0.00134
Other	0.00196	0.00196

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: 0.886
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.73

Haploinsufficiency Scores

• pHI: 0.0662
• hipred: N
• hipred_score: 0.112
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

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