ZNF639

zinc finger protein 639, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:179323031-179338583

Links

ENSG00000121864 ∙ NCBI:51193 ∙ OMIM:619214 ∙ HGNC:30950 ∙ Uniprot:Q9UID6 ∙ 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 ZNF639 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF639 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in ZNF639

This is a list of pathogenic ClinVar variants found in the ZNF639 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-179329621-C-A		not specified	Uncertain significance (Jun 05, 2023)
3-179329720-A-G		not specified	Uncertain significance (May 18, 2022)
3-179332991-G-A		not specified	Uncertain significance (Jun 29, 2022)
3-179333018-G-T		not specified	Uncertain significance (May 25, 2022)
3-179333103-A-G		not specified	Uncertain significance (Sep 30, 2021)
3-179333281-A-G		not specified	Uncertain significance (Jan 18, 2022)
3-179333428-C-G		not specified	Uncertain significance (May 18, 2023)
3-179333719-C-T		not specified	Uncertain significance (Oct 05, 2023)
3-179333764-A-T		not specified	Uncertain significance (Dec 15, 2023)
3-179333805-G-A		not specified	Uncertain significance (Jan 03, 2022)
3-179334034-G-A		not specified	Uncertain significance (Dec 30, 2023)
3-179334315-G-A		not specified	Uncertain significance (Aug 11, 2022)
3-179334338-G-C		not specified	Uncertain significance (Apr 07, 2022)
3-179334414-A-G		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF639	protein_coding	protein_coding	ENST00000326361	4	12545

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000542	0.975	125719	0	19	125738	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	187	242	0.771	0.0000111	3286
Missense in Polyphen		58	107.4	0.54004		1478
Synonymous	0.0538	84	84.6	0.993	0.00000397	809
Loss of Function	1.99	8	16.8	0.477	7.62e-7	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000361	0.0000352
Middle Eastern	0.000113	0.000109
South Asian	0.000174	0.000163
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds DNA and may function as a transcriptional repressor. {ECO:0000269|PubMed:16182284}.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.470
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.254
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp639

Gene ontology

• Biological process: positive regulation of cell growth;negative regulation by host of viral transcription;positive regulation by host of viral transcription;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;viral entry into host cell
• 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 transcription factor activity;protein binding;protein self-association;transcription regulatory region DNA binding;metal ion binding