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SERINC2 serine incorporator 2 [ Homo sapiens (human) ]

Gene ID: 347735, updated on 5-Mar-2024

Summary

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Official Symbol
SERINC2provided by HGNC
Official Full Name
serine incorporator 2provided by HGNC
Primary source
HGNC:HGNC:23231
See related
Ensembl:ENSG00000168528 MIM:614549; AllianceGenome:HGNC:23231
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
TDE2; TDE2L; FKSG84; PRO0899
Summary
Predicted to be involved in several processes, including phosphatidylserine metabolic process; positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity; and positive regulation of serine C-palmitoyltransferase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in urinary bladder (RPKM 35.4), colon (RPKM 35.3) and 17 other tissues See more
Orthologs
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Genomic context

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Location:
1p35.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31409777..31434678)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31262102..31291896)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31882624..31907525)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903892 Neighboring gene Sharpr-MPRA regulatory region 3310 Neighboring gene uncharacterized LOC105378623 Neighboring gene Sharpr-MPRA regulatory region 2178 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:31885808-31886308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31887579-31888127 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 569 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31897069-31897630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31897631-31898192 Neighboring gene uncharacterized LOC124903900 Neighboring gene MS1 minisatellite repeat instability region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31907359-31908163 Neighboring gene uncharacterized LOC105378625 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:31926120-31927319 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:31943609-31944808 Neighboring gene uncharacterized LOC105379772

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. SERINC2 increases the risk of bipolar disorder in the Chinese population. Yang D, et al. Depress Anxiety, 2021 Sep. PMID 34288243
  2. Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder. Hnoonual A, et al. Sci Rep, 2017 Sep 21. PMID 28935972, Free PMC Article
  3. Rare SERINC2 variants are specific for alcohol dependence in individuals of European descent. Zuo L, et al. Pharmacogenet Genomics, 2013 Aug. PMID 23778322, Free PMC Article
  4. Localization to detergent-resistant membranes and HIV-1 core entry inhibition correlate with HIV-1 restriction by SERINC5. Schulte B, et al. Virology, 2018 Feb. PMID 29268082, Free PMC Article
  5. siRNA-mediated knockdown of hTDE2 retards cell cycle progression through transcriptional activation of p21. Ren WH, et al. Oncol Rep, 2014 Mar. PMID 24424505

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SERINC2 increases the risk of bipolar disorder in the Chinese population.
    Title: SERINC2 increases the risk of bipolar disorder in the Chinese population.
  2. Results suggest that the serine incorporator 2 (SERINC2) gene is a novel autism spectrum disorder (ASD) candidate gene.
    Title: Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder.
  3. In contrast to human SERINC5(S5), we observed that human SERINC2(S2) did not restrict HIV-1, and was inefficiently incorporated into HIV-1 virions when compared to S5.
    Title: Localization to detergent-resistant membranes and HIV-1 core entry inhibition correlate with HIV-1 restriction by SERINC5.
  4. TDE2 may have an effect on tumor cell growth by influencing the expression of SREBP and p21.
    Title: siRNA-mediated knockdown of hTDE2 retards cell cycle progression through transcriptional activation of p21.
  5. In subjects of European descent, SERINC2-NKAIN1 expression of genes is associated with alcohol dependence.
    Title: NKAIN1-SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent.
  6. study concluded that SERINC2 was a replicable and significant risk gene specific for alcohol dependence in individuals of European descent
    Title: Rare SERINC2 variants are specific for alcohol dependence in individuals of European descent.
  7. SERINC2 protein localizes in lysosomes in HeLa cells
    Title: Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways.
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

EBI GWAS Catalog

Description
NKAIN1-SERINC2 is a functional, replicable and genome-wide significant risk gene region specific for alcohol dependence in subjects of European descent.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC90340

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
serine incorporator 2
Names
tumor differentially expressed protein 2

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_001199037.2 → NP_001185966.1  serine incorporator 2 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate 5' exon compared to variant 1. The resulting isoform (3) has a longer and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AC114494, AK298512, BC007375, BC084580, BM924335, DC363849
    Consensus CDS
    CCDS55584.1
    Related
    ENSP00000444307.1, ENST00000536859.5
    Conserved Domains (1) summary
    pfam03348
    Location:21 → 457
    Serinc; Serine incorporator (Serinc)

  2. NM_001199038.2 → NP_001185967.1  serine incorporator 2 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has an alternate 5' sequence compared to variant 1. The resulting isoform (4) has a longer and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AK127659, BC007375, BC084580, BM924335
    Consensus CDS
    CCDS55583.1
    Related
    ENSP00000362814.1, ENST00000373710.5
    Conserved Domains (1) summary
    pfam03348
    Location:26 → 462
    Serinc; Serine incorporator (Serinc)

  3. NM_001199039.2 → NP_001185968.1  serine incorporator 2 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) has an alternate 5' exon, resulting in a downstream AUG start codon, compared to variant 1. The resulting isoform (5) has a shorter N-terminus, as compared to isoform 1.
    Source sequence(s)
    AC114494, AK093784, BC007375, BC084580
    Related
    ENST00000491976.1
    Conserved Domains (1) summary
    pfam03348
    Location:1 → 398
    Serinc; Serine incorporator (Serinc)

  4. NM_018565.4 → NP_061035.2  serine incorporator 2 isoform 2

    See identical proteins and their annotated locations for NP_061035.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate 5' exon compared to variant 1. The resulting isoform (2) has a longer and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AK316357, BC007375, BC084580, BM924335
    Consensus CDS
    CCDS55585.1
    Related
    ENSP00000439048.1, ENST00000536384.2
    Conserved Domains (1) summary
    pfam03348
    Location:21 → 457
    Serinc; Serine incorporator (Serinc)

  5. NM_178865.5 → NP_849196.2  serine incorporator 2 isoform 1

    See identical proteins and their annotated locations for NP_849196.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) is a predominant transcript and encodes isoform (1).
    Source sequence(s)
    AK127659, AY094595, BC007375, BC084580, BM924335
    Consensus CDS
    CCDS30662.1
    UniProtKB/Swiss-Prot
    A0AVB4, B4DJK5, B7Z567, B7ZAP2, E7EUZ9, Q86Y23, Q96SA4
    Related
    ENSP00000362813.3, ENST00000373709.8
    Conserved Domains (1) summary
    pfam03348
    Location:17 → 453
    Serinc; Serine incorporator (Serinc)

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    31409777..31434678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    31262102..31291896
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96SA4.3 GenPept UniProtKB/Swiss-Prot:Q96SA4

Gene LinkOut

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