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

Gene ID: 23256, updated on 3-Apr-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, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 19.4), testis (RPKM 13.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
14q12
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (30622254..30735850)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (24820073..24933666)
105.20220307 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
  • 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. 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
  2. Does SCFD1 rs10139154 Polymorphism Decrease Alzheimer's Disease Risk? Stamati P, et al. J Mol Neurosci, 2019 Oct. PMID 31267315
  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. mTOR-mediated phosphorylation of VAMP8 and SCFD1 regulates autophagosome maturation. Huang H, et al. Nat Commun, 2021 Nov 16. PMID 34785650, Free PMC Article

See all (100) 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 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_2023_10

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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