ZNF408 (zinc finger protein 408)

Gene

• Entrez ID: 79797
• Gene name: Zinc finger protein 408
• Gene symbol: ZNF408
• Synonyms (NCBI Gene): EVR6, PRDM17, RP72
• Chromosome: 11
• Chromosome location: 11p11.2
• Summary: The protein encoded by this gene contains ten tandem zinc fingers and an N-terminal SET domain, so it is likely a DNA binding protein that interacts with other proteins. In adults, the encoded protein is expressed most highly in retina. Consequently, defe

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs373273223	C>T	Pathogenic	Missense variant, coding sequence variant
rs774627405	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs781192528	C>T	Pathogenic	Missense variant, coding sequence variant
rs875989821	TG>-	Pathogenic	Frameshift variant, coding sequence variant
rs966073464	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1425566595	T>A	Pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT042778	hsa-miR-339-5p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	14667819, 15231747, 16189514, 18255255, 19060904, 20211142, 25416956, 25910212, 28514442, 32296183, 33961781
GO:0005634	Component	Nucleus	IDA	23716654, 25882705
GO:0005634	Component	Nucleus	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0008270	Function	Zinc ion binding	IEA
GO:0042802	Function	Identical protein binding	IPI	15231747, 18255255, 25416956, 32296183
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 616454
• HGNC: 20041
• e!Ensembl: ENSG00000175213

Protein

• UniProt ID: Q9H9D4
• Protein name: Zinc finger protein 408 (PR domain zinc finger protein 17)
• Protein function: May be involved in transcriptional regulation.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00096	zf-C2H2	381 → 403	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	409 → 431	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	437 → 459	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	468 → 490	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	496 → 518	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	551 → 573	Zinc finger, C2H2 type	Domain
  PF13894	zf-C2H2_4	579 → 602		Domain
  PF00096	zf-C2H2	607 → 629	Zinc finger, C2H2 type	Domain

• Tissue specificity: TISSUE SPECIFICITY: Highest expression is observed in adult retina; abundantly expressed in the fetal eye (PubMed:23716654). In the retina, it is detected in the outer nuclear layer, especially cone and rod photoreceptor cells, ganglion cell layer and bot
• Sequence:

  MEEAEELLLEGKKALQLAREPRLGLDLGWNPSGEGCTQGLKDVPPEPTRDILALKSLPRG
  LALGPSLAKEQRLGVWCVGDPLQPGLLWGPLEEESASKEKGEGVKPRQEENLSLGPWGDV
  CACEQSSGWTSLVQRGRLESEGNVAPVRISERLHLQVYQLVLPGSELLLWPQPSSEGPSL
  TQPGLDKEAAVAVVTEVESAVQQEVASPGEDAAEPCIDPGSQSPSGIQAENMVSPGLKFP
  TQDRISKDSQPLGPLLQDGDVDEECPAQAQMPPELQSNSATQQDPDGSGASFSSSARGTQ
  PHGYLAKKLHSPSDQCPPRAKTPEPGAQQSGFPTLSRSPPGPAGSSPKQGRRYRCGECGK
  AFLQLCHLKKHAFVHTGHKPFLCTECGKSYSSEESFKAHMLGHRGVRPFPCPQCDKAYGT
  QRDLKEHQVVHSGARPFACDQCGKAFARRPSLRLHRKTHQVPAAPAPCPCPVCGRPLANQ
  GSLRNHMRLHTGEKPFLCPHCGRAFRQRGNLRGHLRLHTGERPYRCPHCADAFPQLPELR
  RHLISHTGEAHLCPVCGKALRDPHTLRAHERLHSGERPFPCPQCGRAYTLATKLRRHLKS
  HLEDKPYRCPTCGMGYTLPQSLRRHQLSHRPEAPCSPPSVPSAASEPTVVLLQAEPQLLD
  THREEEVSPARDVVEVTISESQEKCFVVPEEPDAAPSLVLIHKDMGLGAWAEVVEVEMGT
  

• Sequence length: 720

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
Autosomal recessive retinitis pigmentosa	Pathogenic	rs2064733634	RCV001257833	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Exudative vitreoretinopathy 6	Likely pathogenic; Pathogenic	rs373273223, rs781192528, rs1565695139	RCV000186509 RCV002492860 RCV001197448	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Familial exudative vitreoretinopathy	Pathogenic	rs1425566595	RCV001003294	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Likely pathogenic; Pathogenic	rs373273223, rs781192528, rs1384722572, rs1160126418	RCV004816315 RCV001073959 RCV003889570 RCV003889573	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa 72	Pathogenic; Likely pathogenic	rs875989821, rs781192528	RCV000186511 RCV000186512	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
EXUDATIVE VITREORETINOPATHY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Exudative vitreoretinopathy 1	Uncertain significance; Likely benign	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
OPTIC ATROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA	—	Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ZNF408-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations