ZNF536

protein-coding

zinc finger protein 536, the group of Zinc fingers C2H2-type

Gene summary

The protein encoded by this gene is a highly conserved zinc finger protein. The encoded protein is most abundant in brain, where it negatively regulates neuronal differentiation. [provided by RefSeq, Sep 2015]

MANE transcript

NM_014717.3

Inheritance

—

ClinVar variants

P:2U:184B:20

Top phenotype

High myopia

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr19:30,224,891-30,713,586

External References & Databases

Ensembl (ENSG00000198597)

Transcript & Mutation Effects

hg38 • Region Span ~488.7 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 ZNF536 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 162

not providedTotal: 38

High myopiaTotal: 1

Neurodevelopmental disorderTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014717.3. 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	7 clinvar	4 clinvar	12
missense		1 clinvar	170 clinvar	8 clinvar	1 clinvar	180
nonsense			4 clinvar			4
start loss						0
frameshift		1 clinvar	8 clinvar			9
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	2	184	15	5	206

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 67 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014717.3	RefSeq	NP_055532.1	4	MANE Select
ENST00000355537.4	Ensembl	ENSP00000347730.1	4	MANE Select
NM_001352260.2	RefSeq	NP_001339189.1	4	Standard
NM_001376110.1	RefSeq	NP_001363039.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
negative regulation of neuron differentiation
negative regulation of retinoic acid receptor signaling pathway

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription repressor activity, RNA polymerase II-specific
retinoic acid-responsive element binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355537
Coding exons: 4
Length: 485249
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125747
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.40	630	824	0.764	0.0000550	8528
Missense (PolyPhen)		205	403.2	0.50844		4126
Synonymous	0.0400	382	383	0.997	0.0000297	2603
Loss of Function	5.06	3	35.6	0.0843	0.00000153	448

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation. Recognizes and binds 2 copies of the core DNA sequence 5'-CCCCCA- 3'.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.0816
RVIS EVS: -1.57
RVIS percentile EVS: 3.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.262

Gene Damage Prediction

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