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PHAF1 phagosome assembly factor 1 [ Homo sapiens (human) ]

Gene ID: 80262, updated on 5-Mar-2024

Summary

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Official Symbol
PHAF1provided by HGNC
Official Full Name
phagosome assembly factor 1provided by HGNC
Primary source
HGNC:HGNC:29564
See related
Ensembl:ENSG00000125149 AllianceGenome:HGNC:29564
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
LIN10; MYTHO; lin-10; C16orf6; C16orf70
Summary
Predicted to be involved in Golgi to plasma membrane protein transport. Located in phagophore assembly site. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in skin (RPKM 9.9), liver (RPKM 9.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16q22.1
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (67109941..67148544)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72904233..72942836)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67143844..67182447)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 543, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7577 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7578 Neighboring gene core-binding factor subunit beta Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67142676-67143418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67143419-67144160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67189519-67190420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7584 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67195788-67196300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67196374-67197322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67197323-67198271 Neighboring gene TNFRSF1A associated via death domain Neighboring gene F-box and leucine rich repeat protein 8 Neighboring gene heat shock transcription factor 4

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. Kinesin superfamily motor protein KIF17 and mLin-10 in NMDA receptor-containing vesicle transport. Setou M, et al. Science, 2000 Jun 9. PMID 10846156
  2. Mammalian BCAS3 and C16orf70 associate with the phagophore assembly site in response to selective and non-selective autophagy. Kojima W, et al. Autophagy, 2021 Aug. PMID 33499712, Free PMC Article
  3. Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph. Casabonne D, et al. Haematologica, 2011 Feb. PMID 21048031, Free PMC Article
  4. Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity. Hosgood HD 3rd, et al. Occup Environ Med, 2009 Dec. PMID 19773279, Free PMC Article
  5. Generation and analysis of 280,000 human expressed sequence tags. Hillier LD, et al. Genome Res, 1996 Sep. PMID 8889549

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph.
  2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ12076

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi to plasma membrane protein transport IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in dendrite IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in phagophore assembly site IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
phagosome assembly factor 1
Names
UPF0183 protein C16orf70
macro-autophagy and youth optimizer

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_001320540.2 → NP_001307469.1  phagosome assembly factor 1 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
    Source sequence(s)
    AA127668, AL540304, BC004556, HY157930
    Consensus CDS
    CCDS10828.1
    UniProtKB/Swiss-Prot
    Q9BSU1, Q9HA86
    Conserved Domains (1) summary
    pfam03676
    Location:15 → 407
    UPF0183; Uncharacterized protein family (UPF0183)

  2. NM_001320541.2 → NP_001307470.1  phagosome assembly factor 1 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
    Source sequence(s)
    AA127668, BC004556, CB997191, HY157930
    Consensus CDS
    CCDS10828.1
    UniProtKB/Swiss-Prot
    Q9BSU1, Q9HA86
    Conserved Domains (1) summary
    pfam03676
    Location:15 → 407
    UPF0183; Uncharacterized protein family (UPF0183)

  3. NM_001320542.2 → NP_001307471.1  phagosome assembly factor 1 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
    Source sequence(s)
    AA127668, AF176088, BC004556, HY157930
    Consensus CDS
    CCDS10828.1
    UniProtKB/Swiss-Prot
    Q9BSU1, Q9HA86
    Related
    ENSP00000455182.1, ENST00000569600.5
    Conserved Domains (1) summary
    pfam03676
    Location:15 → 407
    UPF0183; Uncharacterized protein family (UPF0183)

  4. NM_001320543.2 → NP_001307472.1  phagosome assembly factor 1 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AA127668, BC004556, CB997191, HY157930
    UniProtKB/Swiss-Prot
    Q9BSU1
    Conserved Domains (1) summary
    pfam03676
    Location:15 → 379
    UPF0183; Uncharacterized protein family (UPF0183)

  5. NM_025187.5 → NP_079463.2  phagosome assembly factor 1 isoform a

    See identical proteins and their annotated locations for NP_079463.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2, 3, and 4 all encode the same isoform (a).
    Source sequence(s)
    AA127668, AC074143, BC004556, HY121038
    Consensus CDS
    CCDS10828.1
    UniProtKB/Swiss-Prot
    Q9BSU1, Q9HA86
    Related
    ENSP00000219139.3, ENST00000219139.8
    Conserved Domains (1) summary
    pfam03676
    Location:15 → 407
    UPF0183; Uncharacterized protein family (UPF0183)

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
    67109941..67148544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006721284.4 → XP_006721347.1  phagosome assembly factor 1 isoform X1

    Conserved Domains (1) summary
    pfam03676
    Location:15 → 504
    UPF0183; uncharacterized protein family (UPF0183)

  2. XM_017023729.2 → XP_016879218.1  phagosome assembly factor 1 isoform X1

    Conserved Domains (1) summary
    pfam03676
    Location:15 → 504
    UPF0183; uncharacterized protein family (UPF0183)

  3. XM_047434712.1 → XP_047290668.1  phagosome assembly factor 1 isoform X4

  4. XM_047434713.1 → XP_047290669.1  phagosome assembly factor 1 isoform X5

  5. XM_017023731.2 → XP_016879220.1  phagosome assembly factor 1 isoform X5

  6. XM_011523350.4 → XP_011521652.1  phagosome assembly factor 1 isoform X2

    Conserved Domains (1) summary
    pfam03676
    Location:17 → 499
    UPF0183; uncharacterized protein family (UPF0183)

  7. XM_047434711.1 → XP_047290667.1  phagosome assembly factor 1 isoform X3

  8. XM_047434714.1 → XP_047290670.1  phagosome assembly factor 1 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    72904233..72942836
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314038.1 → XP_054170013.1  phagosome assembly factor 1 isoform X1

  2. XM_054314039.1 → XP_054170014.1  phagosome assembly factor 1 isoform X1

  3. XM_054314042.1 → XP_054170017.1  phagosome assembly factor 1 isoform X4

  4. XM_054314044.1 → XP_054170019.1  phagosome assembly factor 1 isoform X5

  5. XM_054314043.1 → XP_054170018.1  phagosome assembly factor 1 isoform X5

  6. XM_054314045.1 → XP_054170020.1  phagosome assembly factor 1 isoform X6

  7. XM_054314040.1 → XP_054170015.1  phagosome assembly factor 1 isoform X2

  8. XM_054314041.1 → XP_054170016.1  phagosome assembly factor 1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BSU1.1 GenPept UniProtKB/Swiss-Prot:Q9BSU1

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