SUPT20H (SPT20 homolog, SAGA complex component)

Gene

• Entrez ID: 55578
• Gene name: SPT20 homolog, SAGA complex component
• Gene symbol: SUPT20H
• Synonyms (NCBI Gene): C13, C13orf19, FAM48A, FP757, P38IP, SPT20
• Chromosome: 13
• Chromosome location: 13q13.3

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1566328963	T>A	Risk-factor	Stop gained, coding sequence variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT052010	hsa-let-7b-5p	CLASH	23622248
MIRT039729	hsa-miR-615-3p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000124	Component	SAGA complex	IBA
GO:0000124	Component	SAGA complex	IEA
GO:0000124	Component	SAGA complex	NAS	19114550
GO:0003712	Function	Transcription coregulator activity	IBA
GO:0003712	Function	Transcription coregulator activity	IEA
GO:0005515	Function	Protein binding	IPI	16713569, 16751104, 19893488, 20936779, 21988832, 32814053
GO:0005634	Component	Nucleus	IEA
GO:0006282	Process	Regulation of DNA repair	NAS	11564863
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006914	Process	Autophagy	IEA
GO:0007369	Process	Gastrulation	IEA
GO:0043484	Process	Regulation of RNA splicing	NAS	11564863
GO:0045893	Process	Positive regulation of DNA-templated transcription	NAS	18206972
GO:0070461	Component	SAGA-type complex	IDA	18838386

Other IDs

• MIM: 613417
• HGNC: 20596
• e!Ensembl: ENSG00000102710

Protein

• UniProt ID: Q8NEM7
• Protein name: Transcription factor SPT20 homolog (p38-interacting protein) (p38IP)
• Protein function: Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down-regulation of E-cadherin during gastrulation by regulating E-cadherin protein level downstream from NCK-interacting kinase (NIK)
• PDB: 7KTR, 7KTS, 8H7G
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF12090	Spt20	61 → 161	Spt20 family	Family
  PF12090	Spt20	154 → 228	Spt20 family	Family

• Tissue specificity: TISSUE SPECIFICITY: Highly expressed in testis, moderately in brain and pituitary gland. Expressed in several fetal tissues, including lung, brain, thymus and kidney. Expression is down-regulated in malignant prostate tissues. {ECO:0000269|PubMed:11340631
• Sequence:

  MQQALELALDRAEYVIESARQRPPKRKYLSSGRKSVFQKLYDLYIEECEKEPEVKKLRRN
  VNLLEKLVMQETLSCLVVNLYPGNEGYSLMLRGKNGSDSETIRLPYEEGELLEYLDAEEL
  PPILVDLLEKSQVNIFHCGCVIAEIRDYRQSSNMKSPGYQSRHILLRPTMQTLICDVHSI
  TSDNHKWTQEDKLLLESQLILATAEPLCLDPSIAVTCTANRLLYNKQKMNTRPMKRCFKR
  YSRSSLNRQQDLSHCPPPPQLRLLDFLQKRKERKAGQHYDLKISKAGNCVDMWKRSPCNL
  AIPSEVDVEKYAKVEKSIKSDDSQPTVWPAHDVKDDYVFECEAGTQYQKTKLTILQSLGD
  PLYYGKIQPCKADEESDSQMSPSHSSTDDHSNWFIIGSKTDAERVVNQYQELVQNEAKCP
  VKMSHSSSGSASLSQVSPGKETDQTETVSVQSSVLGKGVKHRPPPIKLPSSSGNSSSGNY
  FTPQQTSSFLKSPTPPPSSKPSSIPRKSSVDLNQVSMLSPAALSPASSSQRTTATQVMAN
  SAGLNFINVVGSVCGAQALMSGSNPMLGCNTGAITPAGINLSGLLPSGGLLPNALPSAMQ
  AASQAGVPFGLKNTSSLRPLNLLQLPGGSLIFNTLQQQQQQLSQFTPQQPQQPTTCSPQQ
  PGEQGSEQGSTSQEQALSAQQAAVINLTGVGSFMQSQAAVLSQLGSAENRPEQSLPQQRF
  QLSSAFQQQQQQIQQLRFLQHQMAMAAAAAQTAQLHHHRHTGSQSKSKMKRGTPTTPKF

• Sequence length: 779

Pathways

KEGG:

Autophagy - animal

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Rheumatoid arthritis	risk factor	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	10987294		★☆☆☆☆ Found in Text Mining only
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	30845214	Stimulate	★☆☆☆☆ Found in Text Mining only
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	30845214	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	9935232		★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	15978328		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	10592101		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	9935232		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of kidney	Kidney Cancer	BEFREE	15978328		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	16685401		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	15978328		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	BEFREE	12200383		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	14722288		★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	15978328, 16685401		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic Neoplasms	LHGDN	11340631		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	BEFREE	30845214		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Rheumatoid Arthritis	Rheumatoid arthritis	CLINVAR_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	27531877		★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	19911042	Associate	★☆☆☆☆ Found in Text Mining only