ZNF513

protein-coding

zinc finger protein 513, the group of Zinc fingers C2H2-type

Gene summary

The protein encoded by this gene is a possible transcriptional regulator involved in retinal development. Defects in this gene can be a cause of autosomal-recessive retinitis pigmentosa. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]

MANE transcript

NM_144631.6

Inheritance

AD, AR

ClinVar variants

P:3U:302B:152

Top phenotype

Retinitis pigmentosa 58

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr2:27,377,235-27,380,790

External References & Databases

Ensembl (ENSG00000163795)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019200

Submitter: Orphanet

retinitis pigmentosa 58MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0013328

Submitter: PanelApp Australia

retinitis pigmentosa 58LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0013328

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Retinitis pigmentosa 58AR

Manifestation: Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 20797688; 20227676

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF513 variants in ClinVar

7 Conditions Cataloged

not providedTotal: 450

not specifiedTotal: 147

Retinitis pigmentosaTotal: 28

Retinal dystrophyTotal: 19

ZNF513-related disorderTotal: 13

Retinitis pigmentosa 58Total: 6

Optic atrophyTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144631.6. 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			5 clinvar	142 clinvar		147
missense		1 clinvar	285 clinvar	10 clinvar		296
nonsense			3 clinvar			3
start loss						0
frameshift	1 clinvar	1 clinvar	5 clinvar			7
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	1	2	302	152	0	457

Highest pathogenic variant AF is 0.00010536258

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144631.6	RefSeq	NP_653232.3	4	MANE Select
ENST00000323703.11	Ensembl	ENSP00000318373.6	4	MANE Select
NM_001201459.2	RefSeq	NP_001188388.1	3	Standard
ENST00000407879.1	Ensembl	ENSP00000384874.1	3	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
znf513a	Danio rerio	Structure: retinal rod cell Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

znf513a

Danio rerio

Structure: retinal rod cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
visual perception
regulation of gene expression
response to stimulus
retina development in camera-type eye

Molecular Function

RNA polymerase II core promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
transcription regulatory region DNA binding

Cellular Component

nucleus
histone methyltransferase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000323703
Coding exons: 4
Length: 3560
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125748
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.530	313	341	0.919	0.0000228	3470
Missense (PolyPhen)		49	41.479	1.1813		377
Synonymous	-2.33	172	137	1.25	0.00000815	1174
Loss of Function	3.37	3	18.8	0.160	0.00000116	201

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000081	0.000079	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional regulator that plays a role in retinal development and maintenance. {ECO:0000269|PubMed:20797688}.;

Intolerance Scores

LoFtool: 0.204
RVIS EVS: -0.44
RVIS percentile EVS: 24.53

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.969

Gene Damage Prediction

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