ZNF215

protein-coding

zinc finger protein 215, the group of Zinc fingers C2H2-type|SCAN domain containing

Gene summary

This gene is imprinted in a tissue-specific manner with preferential expression in the testis, and encodes a zinc finger protein that belongs to a family of zinc finger transcription factors. The encoded protein contains an N-terminal SRE-ZBP, Ctfin51, AW-1, and Number 18 (SCAN) domain, a kruppel-associated box A (KRABA) domain, and four C-terminal zinc finger domains. This gene is located within one of three regions on chromosome 11p15 associated with Beckwith-Wiedemann syndrome, called Beckwith-Wiedemann syndrome chromosome region-2 (BWSCR2), and is thought to play a role in the etiology of this disease. [provided by RefSeq, Aug 2017]

MANE transcript

NM_013250.4

Inheritance

—

ClinVar variants

U:81B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.96

Max pathogenic AF

—

Genomic locus

chr11:6,926,404-7,001,004

External References & Databases

Ensembl (ENSG00000149054)

Transcript & Mutation Effects

hg38 • Region Span ~74.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Beckwith-Wiedemann syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007534

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF215 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013250.4. 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				1 clinvar		1
missense			81 clinvar	9 clinvar	3 clinvar	93
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)				1 clinvar		1
Total	0	0	81	11	3	95

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013250.4	RefSeq	NP_037382.2	5	MANE Select
ENST00000278319.10	Ensembl	ENSP00000278319.5	5	MANE Select
NM_001354853.2	RefSeq	NP_001341782.1	5	Standard
NM_001354854.1	RefSeq	NP_001341783.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
DNA-binding transcription factor activity
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000278319
Coding exons: 5
Length: 58229
Individuals with no LoFs: 125335
Homozygous LoFs: 2
Heterozygous LoFs: 404
Defined: 125741
p: 0.00162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.18	323	269	1.20	0.0000132	3466
Missense (PolyPhen)		74	75.289	0.98287		972
Synonymous	-0.254	96	92.9	1.03	0.00000436	909
Loss of Function	0.193	24	25.0	0.958	0.00000160	271

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00086	0.00086	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.0014	0.0014	notable
East Asian	0.00049	0.00049	rare
Finnish	0.0019	0.0019	notable
European (Non-Finnish)	0.0026	0.0025	notable
South Asian	0.00040	0.00039	rare
Other	0.0023	0.0023	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.0725

Intolerance Scores

LoFtool: 0.958
RVIS EVS: 0.8
RVIS percentile EVS: 87.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00212

Gene Damage Prediction

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