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    SCFD1 sec1 family domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 23256, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SCFD1provided by HGNC
    Official Full Name
    sec1 family domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:20726
    See related
    Ensembl:ENSG00000092108 MIM:618207; AllianceGenome:HGNC:20726
    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
    SLY1; RA410; SLY1P; STXBP1L2; C14orf163
    Summary
    Predicted to enable syntaxin binding activity. Involved in negative regulation of autophagosome assembly; regulation of protein transport; and response to toxic substance. Located in cis-Golgi network. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 19.4), testis (RPKM 13.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SCFD1 in Genome Data Viewer
    Location:
    14q12
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (30622254..30735850)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (24820073..24933666)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (31091460..31205056)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene G2E3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8224 Neighboring gene SYF2 pre-mRNA splicing factor pseudogene 1 Neighboring gene G2/M-phase specific E3 ubiquitin protein ligase Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:31090859-31092058 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:31143443-31144642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8226 Neighboring gene NANOG hESC enhancer GRCh37_chr14:31161751-31162310 Neighboring gene ubiquitin conjugating enzyme E2 C pseudogene 1 Neighboring gene ribosomal protein L12 pseudogene 5 Neighboring gene ribosomal protein L27 pseudogene 1

    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 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. Does SCFD1 rs10139154 Polymorphism Decrease Alzheimer's Disease Risk? Stamati P, et al. J Mol Neurosci, 2019 Oct. PMID 31267315
    2. Lack of an association between SCFD1 rs10139154 polymorphism and amyotrophic lateral sclerosis. Siokas V, et al. Mol Med Rep, 2022 Apr. PMID 35234271, Free PMC Article
    3. An association study between SCFD1 rs10139154 variant and amyotrophic lateral sclerosis in a Chinese cohort. Chen Y, et al. Amyotroph Lateral Scler Frontotemporal Degener, 2018 Aug. PMID 29260601
    4. RA410/Sly1 suppresses MPP+ and 6-hydroxydopamine-induced cell death in SH-SY5Y cells. Bando Y, et al. Neurobiol Dis, 2005 Feb. PMID 15649705
    5. rsly1 binding to syntaxin 5 is required for endoplasmic reticulum-to-Golgi transport but does not promote SNARE motif accessibility. Williams AL, et al. Mol Biol Cell, 2004 Jan. PMID 14565970, Free PMC Article

    See all (110) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Lack of an association between SCFD1 rs10139154 polymorphism and amyotrophic lateral sclerosis.
      Title: Lack of an association between SCFD1 rs10139154 polymorphism and amyotrophic lateral sclerosis.
    2. mTOR-mediated phosphorylation of VAMP8 and SCFD1 regulates autophagosome maturation.
      Title: mTOR-mediated phosphorylation of VAMP8 and SCFD1 regulates autophagosome maturation.
    3. SCFD1 rs10139154 is associated with a decreased risk of developing Alzheimer disease.
      Title: Does SCFD1 rs10139154 Polymorphism Decrease Alzheimer's Disease Risk?
    4. The found of this study confirmed the lack of association of SCFD1 rs10139154 with the risk for ALS in a large Chinese population.
      Title: An association study between SCFD1 rs10139154 variant and amyotrophic lateral sclerosis in a Chinese cohort.
    5. Mutation in SCFD1 gene is associated with amyotrophic lateral sclerosis.
      Title: Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Study shows that the SM protein, Sly1, interacts directly with the conserved oligomeric Golgi (COG) tethering complex; Sly1-COG interaction is mediated by the Cog4 subunit, which also interacts with Syntaxin 5 through a different binding site.
      Title: Direct interaction between the COG complex and the SM protein, Sly1, is required for Golgi SNARE pairing.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of sec1 family domain containing 1 (SCFD1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0917

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables syntaxin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables syntaxin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in post-Golgi vesicle-mediated transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of ER to Golgi vesicle-mediated transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of protein transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to toxic substance IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi cisterna membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi-associated vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cis-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    sec1 family domain-containing protein 1
    Names
    syntaxin-binding protein 1-like 2
    vesicle transport-related 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_001257376.1 → NP_001244305.1  sec1 family domain-containing protein 1 isoform c

      See identical proteins and their annotated locations for NP_001244305.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AK298622, BG212062, DA151789
      Consensus CDS
      CCDS58308.1
      UniProtKB/TrEMBL
      A0A7I2V4R0
      Related
      ENSP00000379870.2, ENST00000396629.6
      Conserved Domains (1) summary
      pfam00995
      Location:1 → 537
      Sec1; Sec1 family

    2. NM_001283031.1 → NP_001269960.1  sec1 family domain-containing protein 1 isoform d

      See identical proteins and their annotated locations for NP_001269960.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an exon in the 5' region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus, compared to isoform a. Variants 4 and 6 encode the same isoform (d).
      Source sequence(s)
      AK299222, BG212062, DB105324
      Consensus CDS
      CCDS91858.1
      UniProtKB/TrEMBL
      A0A7I2V448, B7Z5N7
      Related
      ENSP00000504658.1, ENST00000676520.1
      Conserved Domains (1) summary
      pfam00995
      Location:3 → 444
      Sec1; Sec1 family

    3. NM_001283032.1 → NP_001269961.1  sec1 family domain-containing protein 1 isoform e

      See identical proteins and their annotated locations for NP_001269961.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an exon in the 5' region and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (e) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AF067205, AK301406, BG212062, BX325898, DB105324
      UniProtKB/TrEMBL
      A0A7I2V4R0, B7Z738
      Conserved Domains (1) summary
      pfam00995
      Location:16 → 570
      Sec1; Sec1 family

    4. NM_001283033.1 → NP_001269962.1  sec1 family domain-containing protein 1 isoform d

      See identical proteins and their annotated locations for NP_001269962.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks three exons in the 5' region and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus, compared to isoform a. Variants 4 and 6 encode the same isoform (d).
      Source sequence(s)
      AK307960, BG212062, DB105324, DN993082
      Consensus CDS
      CCDS91858.1
      UniProtKB/TrEMBL
      A0A7I2V448, B7Z5N7
      Related
      ENSP00000502860.1, ENST00000676674.1
      Conserved Domains (1) summary
      pfam00995
      Location:3 → 444
      Sec1; Sec1 family

    5. NM_016106.4 → NP_057190.2  sec1 family domain-containing protein 1 isoform a

      See identical proteins and their annotated locations for NP_057190.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AB020724, AL121852, BG212062
      Consensus CDS
      CCDS9639.1
      UniProtKB/Swiss-Prot
      A8K2Z5, B7Z4U7, B7Z594, O60754, O94990, Q7Z529, Q8WVM8, Q9BZI3, Q9UNL3, Q9Y6A8
      UniProtKB/TrEMBL
      A0A7I2V5Z4, Q53GW1
      Related
      ENSP00000390783.2, ENST00000458591.7
      Conserved Domains (1) summary
      pfam00995
      Location:44 → 629
      Sec1; Sec1 family

    6. NM_182835.2 → NP_878255.1  sec1 family domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_878255.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AK316212, BG212062, DB105324
      Consensus CDS
      CCDS45092.1
      UniProtKB/TrEMBL
      A0A7I2V4R0
      Related
      ENSP00000443010.2, ENST00000544052.6
      Conserved Domains (1) summary
      pfam00995
      Location:1 → 562
      Sec1; Sec1 family

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      30622254..30735850
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431165.1 → XP_047287121.1  sec1 family domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A7I2V590
      Related
      ENSP00000504310.1, ENST00000678399.1

    2. XM_047431166.1 → XP_047287122.1  sec1 family domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      H0YIZ7
      Related
      ENSP00000450546.2, ENST00000554437.6

    3. XM_017021113.3 → XP_016876602.1  sec1 family domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A7I2YQR2
      Related
      ENSP00000504309.1, ENST00000678760.1

    4. XM_005267469.3 → XP_005267526.1  sec1 family domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005267526.1

      UniProtKB/TrEMBL
      A0A7I2V4R0
      Related
      ENSP00000504124.1, ENST00000677340.1
      Conserved Domains (1) summary
      pfam00995
      Location:19 → 604
      Sec1; Sec1 family

    RNA

    1. XR_007063993.1 RNA Sequence

    2. XR_007063994.1 RNA Sequence

    3. XR_007063995.1 RNA Sequence

    4. XR_007063996.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      24820073..24933666
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375710.1 → XP_054231685.1  sec1 family domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A7I2V590

    2. XM_054375711.1 → XP_054231686.1  sec1 family domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      H0YIZ7

    3. XM_054375712.1 → XP_054231687.1  sec1 family domain-containing protein 1 isoform X4

    4. XM_054375709.1 → XP_054231684.1  sec1 family domain-containing protein 1 isoform X1

    RNA

    1. XR_008488830.1 RNA Sequence

    2. XR_008488831.1 RNA Sequence

    3. XR_008488832.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WVM8.4 GenPept UniProtKB/Swiss-Prot:Q8WVM8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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