ZNF639

protein-coding

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

Gene summary

This gene encodes a member of the Kruppel-like zinc finger family of proteins. Amplification and overexpression of this gene have been observed in esophageal squamous cell carcinoma. The encoded protein has been shown to bind DNA in a sequence-specific manner and may regulate HIV-1 gene expression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

MANE transcript

NM_001303426.2

Inheritance

—

ClinVar variants

U:42

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr3:179,323,031-179,338,583

External References & Databases

Ensembl (ENSG00000121864)

Transcript & Mutation Effects

hg38 • Region Span ~15.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF639 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 41

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001303426.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			41 clinvar			41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	42	0	0	42

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001303426.2	RefSeq	NP_001290355.1	4	MANE Select
ENST00000496856.6	Ensembl	ENSP00000417740.1	4	MANE Select
NM_001303425.2	RefSeq	NP_001290354.1	4	Standard
NM_001375800.1	RefSeq	NP_001362729.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

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

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326361
Coding exons: 4
Length: 12545
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125738
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.27	187	242	0.771	0.0000111	3286
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.00017	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.981

Gene Damage Prediction

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