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

Gene ID: 83449, updated on 3-Apr-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 connecting piece. Implicated in spermatogenic failure 31. [provided by Alliance of Genome Resources, Apr 2022]
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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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (72116657..72249949, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (77931754..78066251, complement)
105.20220307 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. Biallelic mutations in PMFBP1 cause acephalic spermatozoa. Sha YW, et al. Clin Genet, 2019 Feb. PMID 30298696
  4. 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
  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)

Genotypes

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

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
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
  
is_active_in sperm connecting piece IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in sperm connecting piece 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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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_2023_10

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

  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

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

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

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

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

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

  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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