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    PMFBP1 polyamine modulated factor 1 binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 83449, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PMFBP1provided by HGNC
    Official Full Name
    polyamine modulated factor 1 binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:17728
    See related
    Ensembl:ENSG00000118557 MIM:618085; AllianceGenome:HGNC:17728
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    STAP; SPGF31
    Summary
    Involved in spermatogenesis. Located in sperm head-tail coupling apparatus. Implicated in spermatogenic failure 31. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in testis (RPKM 6.6), small intestine (RPKM 0.5) and 2 other tissues See more
    Orthologs
    mouse all
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    Try the new Transcript table

    Genomic context

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    See PMFBP1 in Genome Data Viewer
    Location:
    16q22.2
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (72116657..72249949, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (77931754..78066251, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (72152996..72206369, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11091 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72132901-72133401 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:72141414-72142613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11093 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:72159455-72159956 Neighboring gene NANOG hESC enhancer GRCh37_chr16:72162293-72163093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72163923-72164424 Neighboring gene thioredoxin like 4B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72171124-72171624 Neighboring gene haptoglobin-related protein Neighboring gene DEAH-box helicase 38 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11095 Neighboring gene uncharacterized LOC105371341 Neighboring gene VISTA enhancer hs22 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:72257113-72258312 Neighboring gene uncharacterized LOC124903720 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:72319061-72319706 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:72324412-72325611 Neighboring gene MYC binding protein pseudogene Neighboring gene long intergenic non-protein coding RNA 1572 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44023 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44041 Neighboring gene VISTA enhancer hs108 Neighboring gene uncharacterized LOC124903812

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Patients with acephalic spermatozoa syndrome linked to novel TSGA10/PMFBP1 variants have favorable pregnancy outcomes from intracytoplasmic sperm injection. Liu G, et al. Clin Genet, 2021 Sep. PMID 34089195
    2. A novel homozygous missense mutation of PMFBP1 causes acephalic spermatozoa syndrome. Lu M, et al. J Assist Reprod Genet, 2021 Apr. PMID 33484382, Free PMC Article
    3. Novel mutations in PMFBP1, TSGA10 and SUN5: Expanding the spectrum of mutations that may cause acephalic spermatozoa. Liu G, et al. Clin Genet, 2020 Jun. PMID 32285443
    4. Biallelic mutations in PMFBP1 cause acephalic spermatozoa. Sha YW, et al. Clin Genet, 2019 Feb. PMID 30298696
    5. Mutations in PMFBP1 Cause Acephalic Spermatozoa Syndrome. Zhu F, et al. Am J Hum Genet, 2018 Aug 2. PMID 30032984, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Patients with acephalic spermatozoa syndrome linked to novel TSGA10/PMFBP1 variants have favorable pregnancy outcomes from intracytoplasmic sperm injection.
      Title: Patients with acephalic spermatozoa syndrome linked to novel TSGA10/PMFBP1 variants have favorable pregnancy outcomes from intracytoplasmic sperm injection.
    2. A novel homozygous missense mutation of PMFBP1 causes acephalic spermatozoa syndrome.
      Title: A novel homozygous missense mutation of PMFBP1 causes acephalic spermatozoa syndrome.
    3. Novel mutations in PMFBP1, TSGA10 and SUN5: Expanding the spectrum of mutations that may cause acephalic spermatozoa.
      Title: Novel mutations in PMFBP1, TSGA10 and SUN5: Expanding the spectrum of mutations that may cause acephalic spermatozoa.
    4. our data indicate that PMFBP1 is necessary for sperm morphology in both humans and mice, and that biallelic truncating mutations in PMFBP1 cause acephalic spermatozoa
      Title: Biallelic mutations in PMFBP1 cause acephalic spermatozoa.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Spermatogenic failure 31
    MedGen: C4748234 OMIM: 618112 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of polyamine modulated factor 1 binding protein 1 (PMFBP1) in peptide-treated PBMCs PubMed
    Vif vif HIV-1 Vif downregulates the expression of polyamine modulated factor 1 binding protein 1 (PMFBP1) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ40146, DKFZp434G131

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein-containing complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in sperm flagellum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in sperm head IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in sperm head-tail coupling apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in sperm head-tail coupling apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    polyamine-modulated factor 1-binding protein 1
    Names
    PMF-1 binding protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001160213.2 → NP_001153685.1  polyamine-modulated factor 1-binding protein 1 isoform b

      See identical proteins and their annotated locations for NP_001153685.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR, translation initiation at a downstream AUG codon, and an additional segment in the 3' coding region, compared to variant 1. The encoded protein (isoform b) is shorter than isoform a.
      Source sequence(s)
      AC004682, AF239683, AK093285, AK122925, DB082449
      UniProtKB/TrEMBL
      B2RCA2
      Related
      ENSP00000347854.6, ENST00000355636.10
      Conserved Domains (1) summary
      COG1196
      Location:91 → 718
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    2. NM_031293.3 → NP_112583.2  polyamine-modulated factor 1-binding protein 1 isoform a

      See identical proteins and their annotated locations for NP_112583.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript but encodes the longer isoform (a).
      Source sequence(s)
      AF239683, AK093285, AL136795, DB019901
      Consensus CDS
      CCDS32483.1
      UniProtKB/Swiss-Prot
      B3KVI9, G3V1Q7, H7BY07, Q8NA09, Q8TBY8, Q9BY16, Q9H0H4
      UniProtKB/TrEMBL
      B2RCA2
      Related
      ENSP00000237353.10, ENST00000237353.15
      Conserved Domains (1) summary
      COG1196
      Location:236 → 863
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      72116657..72249949 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434734.1 → XP_047290690.1  polyamine-modulated factor 1-binding protein 1 isoform X3

      UniProtKB/TrEMBL
      B2RCA2

    2. XM_011523361.4 → XP_011521663.1  polyamine-modulated factor 1-binding protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011521663.1

      UniProtKB/TrEMBL
      B2RCA2
      Conserved Domains (3) summary
      COG1196
      Location:505 → 805
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK05771
      Location:695 → 930
      PRK05771; V-type ATP synthase subunit I; Validated
      TIGR02169
      Location:294 → 648
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    3. XM_011523358.4 → XP_011521660.1  polyamine-modulated factor 1-binding protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011521660.1

      UniProtKB/TrEMBL
      B2RCA2
      Conserved Domains (3) summary
      COG1196
      Location:505 → 805
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK05771
      Location:695 → 930
      PRK05771; V-type ATP synthase subunit I; Validated
      TIGR02169
      Location:294 → 648
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    4. XM_011523357.4 → XP_011521659.1  polyamine-modulated factor 1-binding protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011521659.1

      UniProtKB/TrEMBL
      B2RCA2
      Conserved Domains (3) summary
      COG1196
      Location:505 → 805
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK05771
      Location:695 → 930
      PRK05771; V-type ATP synthase subunit I; Validated
      TIGR02169
      Location:294 → 648
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    5. XM_011523360.4 → XP_011521662.1  polyamine-modulated factor 1-binding protein 1 isoform X1

      See identical proteins and their annotated locations for XP_011521662.1

      UniProtKB/TrEMBL
      B2RCA2
      Conserved Domains (3) summary
      COG1196
      Location:505 → 805
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK05771
      Location:695 → 930
      PRK05771; V-type ATP synthase subunit I; Validated
      TIGR02169
      Location:294 → 648
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    6. XM_011523362.4 → XP_011521664.1  polyamine-modulated factor 1-binding protein 1 isoform X2

      UniProtKB/TrEMBL
      B2RCA2
      Conserved Domains (3) summary
      COG1196
      Location:502 → 802
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      PRK05771
      Location:692 → 927
      PRK05771; V-type ATP synthase subunit I; Validated
      TIGR02169
      Location:291 → 645
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    7. XM_047434735.1 → XP_047290691.1  polyamine-modulated factor 1-binding protein 1 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      77931754..78066251 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314089.1 → XP_054170064.1  polyamine-modulated factor 1-binding protein 1 isoform X3

      UniProtKB/TrEMBL
      B2RCA2

    2. XM_054314087.1 → XP_054170062.1  polyamine-modulated factor 1-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      B2RCA2

    3. XM_054314085.1 → XP_054170060.1  polyamine-modulated factor 1-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      B2RCA2

    4. XM_054314084.1 → XP_054170059.1  polyamine-modulated factor 1-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      B2RCA2

    5. XM_054314086.1 → XP_054170061.1  polyamine-modulated factor 1-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      B2RCA2

    6. XM_054314088.1 → XP_054170063.1  polyamine-modulated factor 1-binding protein 1 isoform X2

      UniProtKB/TrEMBL
      B2RCA2

    7. XM_054314090.1 → XP_054170065.1  polyamine-modulated factor 1-binding protein 1 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TBY8.3 GenPept UniProtKB/Swiss-Prot:Q8TBY8

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