ZNF513 (zinc finger protein 513)

Gene

• Entrez ID: 130557
• Gene name: Zinc finger protein 513
• Gene symbol: ZNF513
• Synonyms (NCBI Gene): HMFT0656, RP58, Zfp513
• Chromosome: 2
• Chromosome location: 2p23.3
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs35554630	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, 5 prime UTR variant
rs61742428	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs199520071	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs267607182	A>G	Pathogenic, uncertain-significance	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT001857	hsa-miR-376a-5p	Luciferase reporter assay	17322061
MIRT001857	hsa-miR-376a-5p	Luciferase reporter assay	17322061
MIRT2378829	hsa-miR-331-3p	CLIP-seq
MIRT2378830	hsa-miR-3922-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000976	Function	Transcription cis-regulatory region binding	IBA
GO:0000976	Function	Transcription cis-regulatory region binding	IDA	20797688
GO:0000976	Function	Transcription cis-regulatory region binding	IEA
GO:0003677	Function	DNA binding	IDA	20797688
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 32296183, 32814053
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	20797688
GO:0005634	Component	Nucleus	IEA
GO:0007601	Process	Visual perception	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA
GO:0046872	Function	Metal ion binding	IEA
GO:0060041	Process	Retina development in camera-type eye	IMP	20797688

Other IDs

• MIM: 613598
• HGNC: 26498
• e!Ensembl: ENSG00000163795

Protein

• UniProt ID: Q8N8E2
• Protein name: Zinc finger protein 513
• Protein function: Transcriptional regulator that plays a role in retinal development and maintenance.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00096	zf-C2H2	178 → 200	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	206 → 228	Zinc finger, C2H2 type	Domain
  PF13465	zf-H2C2_2	402 → 427		Domain
  PF00096	zf-C2H2	444 → 466	Zinc finger, C2H2 type	Domain

• Tissue specificity: TISSUE SPECIFICITY: In the retina, expressed in the outer and inner nuclear layers, and the ganglion cell layer. {ECO:0000269|PubMed:20797688}.
• Sequence:

  MPRRKQSHPQPVKCEGVKVDTEDSLDEGPGALVLESDLLLGQDLEFEEEEEEEEGDGNSD
  QLMGFERDSEGDSLGARPGLPYGLSDDESGGGRALSAESEVEEPARGPGEARGERPGPAC
  QLCGGPTGEGPCCGAGGPGGGPLLPPRLLYSCRLCTFVSHYSSHLKRHMQTHSGEKPFRC
  GRCPYASAQLVNLTRHTRTHTGEKPYRCPHCPFACSSLGNLRRHQRTHAGPPTPPCPTCG
  FRCCTPRPARPPSPTEQEGAVPRRPEDALLLPDLSLHVPPGGASFLPDCGQLRGEGEGLC
  GTGSEPLPELLFPWTCRGCGQELEEGEGSRLGAAMCGRCMRGEAGGGASGGPQGPSDKGF
  ACSLCPFATHYPNHLARHMKTHSGEKPFRCARCPYASAHLDNLKRHQRVHTGEKPYKCPL
  CPYACGNLANLKRHGRIHSGDKPFRCSLCNYSCNQSMNLKRHMLRHTGEKPFRCATCAYT
  TGHWDNYKRHQKVHGHGGAGGPGLSASEGWAPPHSPPSVLSSRGPPALGTAGSRAVHTDS
  S

• Sequence length: 541

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Retinitis pigmentosa 58	Likely pathogenic	rs1683490120	RCV001196536	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Optic atrophy	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Retinal dystrophy	Conflicting classifications of pathogenicity; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis pigmentosa	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	ClinVar Disgenet, Orphanet Disgenet, Orphanet Disgenet, Orphanet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis Pigmentosa, Dominant	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ZNF513-related disorder	Likely benign; Uncertain significance; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Arthritis, Gouty	Gouty arthritis	GWASDB_DG	20884846, 23263486		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain Neoplasms	BEFREE	22095278		★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Gout	Gout	GWASDB_DG	20884846, 23263486		★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Keratoconus	Keratoconus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development, Group II	Malformation of cortical development	BEFREE	29501651		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	22095278		★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Periodontitis	Periodontitis	BEFREE	12445647		★☆☆☆☆ Found in Text Mining only
Retinitis pigmentosa	Retinitis Pigmentosa	Orphanet			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	20797688		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Retinitis Pigmentosa	Retinitis Pigmentosa	GENOMICS_ENGLAND_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
RETINITIS PIGMENTOSA 58	Retinitis Pigmentosa	UNIPROT_DG	20797688		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RETINITIS PIGMENTOSA 58	Retinitis Pigmentosa	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RETINITIS PIGMENTOSA 58	Retinitis Pigmentosa	GENOMICS_ENGLAND_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rod-Cone Dystrophy	Rod-cone dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only