PMFBP1 (polyamine modulated factor 1 binding protein 1)

Gene

• Entrez ID: 83449
• Gene name: Polyamine modulated factor 1 binding protein 1
• Gene symbol: PMFBP1
• Synonyms (NCBI Gene): SPGF31, STAP
• Chromosome: 16
• Chromosome location: 16q22.2

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs140352254	G>A	Pathogenic	Coding sequence variant, stop gained
rs759127010	A>T	Pathogenic	Coding sequence variant, 5 prime UTR variant, stop gained
rs769554360	CTTT>-	Pathogenic	Coding sequence variant, frameshift variant
rs772371753	TT>-	Pathogenic	Coding sequence variant, frameshift variant
rs777263062	G>A	Pathogenic	Coding sequence variant, stop gained
rs1567621034	C>-	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2072198	hsa-miR-511	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005737	Component	Cytoplasm	IEA
GO:0005929	Component	Cilium	IEA
GO:0007283	Process	Spermatogenesis	IBA
GO:0007283	Process	Spermatogenesis	IEA
GO:0007283	Process	Spermatogenesis	IMP	30032984
GO:0007286	Process	Spermatid development	IEA
GO:0008104	Process	Intracellular protein localization	IEA
GO:0010467	Process	Gene expression	IEA
GO:0031514	Component	Motile cilium	IEA
GO:0032880	Process	Regulation of protein localization	IEA
GO:0036126	Component	Sperm flagellum	IEA
GO:0042995	Component	Cell projection	IEA
GO:0061827	Component	Sperm head	IEA
GO:0065003	Process	Protein-containing complex assembly	IEA
GO:0120212	Component	Sperm head-tail coupling apparatus	IBA
GO:0120212	Component	Sperm head-tail coupling apparatus	IDA	30032984
GO:0120212	Component	Sperm head-tail coupling apparatus	IEA

Other IDs

• MIM: 618085
• HGNC: 17728
• e!Ensembl: ENSG00000118557

Protein

• UniProt ID: Q8TBY8
• Protein name: Polyamine-modulated factor 1-binding protein 1 (PMF-1-binding protein)
• Protein function: Required for normal spermatogenesis (PubMed:1770140, PubMed:30032984, PubMed:30298696). It functions as a scaffold protein that attaches the sperm head-tail connecting piece to the nuclear envelope, thus maintaining sperm head and tail integrity
• Sequence:

  MKDEAGERDREVSSLNSKLLSLQLDIKNLHDVCKRQRKTLQDNQLCMEEAMNSSHDKKQA
  QALAFEESEVEFGSSKQCHLRQLQQLKKKLLVLQQELEFHTEELQTSYYSLRQYQSILEK
  QTSDLVLLHHHCKLKEDEVILYEEEMGNHNENTGEKLHLAQEQLALAGDKIASLERSLNL
  YRDKYQSSLSNIELLECQVKMLQGELGGIMGQEPENKGDHSKVRIYTSPCMIQEHQETQK
  RLSEVWQKVSQQDDLIQELRNKLACSNALVLEREKALIKLQADFASCTATHRYPPSSSEE
  CEDIKKILKHLQEQKDSQCLHVEEYQNLVKDLRVELEAVSEQKRNIMKDMMKLELDLHGL
  REETSAHIERKDKDITILQCRLQELQLEFTETQKLTLKKDKFLQEKDEMLQELEKKLTQV
  QNSLLKKEKELEKQQCMATELEMTVKEAKQDKSKEAECKALQAEVQKLKNSLEEAKQQER
  LAAQQAAQCKEEAALAGCHLEDTQRKLQKGLLLDKQKADTIQELQRELQMLQKESSMAEK
  EQTSNRKRVEELSLELSEALRKLENSDKEKRQLQKTVAEQDMKMNDMLDRIKHQHREQGS
  IKCKLEEDLQEATKLLEDKREQLKKSKEHEKLMEGELEALRQEFKKKDKTLKENSRKLEE
  ENENLRAELQCCSTQLESSLNKYNTSQQVIQDLNKEIALQKESLMSLQAQLDKALQKEKH
  YLQTTITKEAYDALSRKSAACQDDLTQALEKLNHVTSETKSLQQSLTQTQEKKAQLEEEI
  IAYEERMKKLNTELRKLRGFHQESELEVHAFDKKLEEMSCQVLQWQKQHQNDLKMLAAKE
  EQLREFQEEMAALKENLLEDDKEPCCLPQWSVPKDTCRLYRGNDQIMTNLEQWAKQQKVA
  NEKLGNQLREQVKYIAKLSGEKDHLHSVMVHLQQENKKLKKEIEEKKMKAENTRLCTKAL
  GPSRTESTQREKVCGTLGWKGLPQDMGQRMDLTKYIGMPHCPGSSYC

• Sequence length: 1007

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
Spermatogenic failure 31	Likely pathogenic; Pathogenic	rs767705612, rs763272588, rs777263062, rs140352254, rs1567621034, rs772371753, rs759127010, rs769554360	RCV003223604 RCV003329138 RCV000678506 RCV000678507 RCV000678508 RCV000760139 RCV000760140 RCV000995610	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANOREXIA NERVOSA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC BRONCHITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSLEXIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERLIPIDEMIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IGA GLOMERULONEPHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALE INFERTILITY DUE TO ACEPHALIC SPERMATOZOA	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBSESSIVE-COMPULSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PMFBP1-related disorder	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPECIFIC LANGUAGE IMPAIRMENT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPERMATOGENIC FAILURE 16	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TERATOZOOSPERMIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOURETTE SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VENOUS THROMBOEMBOLISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acephalic spermatozoa	Acephalic spermatozoa	BEFREE	30032984, 30298696		★☆☆☆☆ Found in Text Mining only
Acephalic spermatozoa	Acephalic spermatozoa	HPO_DG			★☆☆☆☆ Found in Text Mining only
Asthenozoospermia	Asthenozoospermia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Azoospermia Nonobstructive	Nonobstructive azoospermia	Pubtator	36017582	Associate	★☆☆☆☆ Found in Text Mining only
Male infertility due to acephalic spermatozoa	Male infertility	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Oligospermia	Oligospermia	HPO_DG			★☆☆☆☆ Found in Text Mining only
SPERMATOGENIC FAILURE 16	Spermatogenic Failure	BEFREE	30032984		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPERMATOGENIC FAILURE 16	Spermatogenic Failure	ORPHANET_DG	30032984		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPERMATOGENIC FAILURE 31	Spermatogenic Failure	ORPHANET_DG	30032984		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SPERMATOGENIC FAILURE 31	Spermatogenic Failure	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)