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FAM3A FAM3 metabolism regulating signaling molecule A [ Homo sapiens (human) ]

Gene ID: 60343, updated on 7-Apr-2024

Summary

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Official Symbol
FAM3Aprovided by HGNC
Official Full Name
FAM3 metabolism regulating signaling molecule Aprovided by HGNC
Primary source
HGNC:HGNC:13749
See related
Ensembl:ENSG00000071889 MIM:300492; AllianceGenome:HGNC:13749
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DLD; 2.19; XAP-7; DXS560S
Summary
This gene encodes a cytokine-like protein. The expression of this gene may be regulated by peroxisome proliferator-activated receptor gamma, and the encoded protein may be involved in the regulation of glucose and lipid metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Expression
Ubiquitous expression in small intestine (RPKM 12.0), fat (RPKM 11.4) and 25 other tissues See more
Orthologs
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Genomic context

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See FAM3A in Genome Data Viewer
Location:
Xq28
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154506171..154516232, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152742672..152752723, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153734502..153744556, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21112 Neighboring gene solute carrier family 10 member 3 Neighboring gene RNA, 7SL, cytoplasmic 697, pseudogene Neighboring gene uncharacterized LOC124905229 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153743824-153744447 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153744448-153745070 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153745046-153745202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30065 Neighboring gene Sharpr-MPRA regulatory region 11639 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153762224-153762818 Neighboring gene glucose-6-phosphate dehydrogenase Neighboring gene G6PD and IKBKG intron CAGE-defined low expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153774097-153774640 Neighboring gene origin of replication in promoter of G6PD Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30067 Neighboring gene inhibitor of nuclear factor kappa B kinase regulatory subunit gamma Neighboring gene IKBKG recombination region Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153792215-153792716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153792717-153793216 Neighboring gene IKBKG downstream recombination region Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153798001-153798800 Neighboring gene family with sequence similarity 223 member A

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. Case report: targeted whole exome sequencing enables the first prenatal diagnosis of the lethal skeletal dysplasia Osteocraniostenosis. Pemberton L, et al. BMC Med Genet, 2020 Jan 7. PMID 31910817, Free PMC Article
  2. Role of Family with Sequence Similarity 3A in High Glucose-induced Oxidative Damage of Human Umbilical Vein Endothelial Cells. Liao PZ, et al. Zhongguo Yi Xue Ke Xue Yuan Xue Bao, 2018 Feb 28. PMID 29532774
  3. Transcriptional regulation analysis of FAM3A gene and its effect on adipocyte differentiation. Kang T, et al. Gene, 2016 Dec 20. PMID 27688071
  4. FAM3A Protects HT22 Cells Against Hydrogen Peroxide-Induced Oxidative Stress Through Activation of PI3K/Akt but not MEK/ERK Pathway. Song Q, et al. Cell Physiol Biochem, 2015. PMID 26492522
  5. Endothelial FAM3A positively regulates post-ischaemic angiogenesis. Xu W, et al. EBioMedicine, 2019 May. PMID 31000420, Free PMC Article

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FAM3A mediates the phenotypic switch of human aortic smooth muscle cells stimulated with oxidised low-density lipoprotein by influencing the PI3K-AKT pathway.
    Title: FAM3A mediates the phenotypic switch of human aortic smooth muscle cells stimulated with oxidised low-density lipoprotein by influencing the PI3K-AKT pathway.
  2. In this case prenatal ultrasound images were suggestive of a serious but non-lethal skeletal dysplasia. Due to the uncertain prognosis the parents were offered Whole Exome Sequencing (WES), which identified a specific gene mutation in the FAMIIIa gene
    Title: Case report: targeted whole exome sequencing enables the first prenatal diagnosis of the lethal skeletal dysplasia Osteocraniostenosis.
  3. our data demonstrate that FAM3A positively regulates angiogenesis through activation of VEGFA transcription, suggesting that FAM3A may constitute a novel molecular therapeutic target for ischaemic vascular disease.
    Title: Endothelial FAM3A positively regulates post-ischaemic angiogenesis.
  4. Fam3A may regulate high glucose-induced reactive oxygen species production in HUVECs via the p38 MAPK signaling pathway.
    Title: Role of Family with Sequence Similarity 3A in High Glucose-induced Oxidative Damage of Human Umbilical Vein Endothelial Cells.
  5. These results suggest that C/EBPbeta plays an important role in regulating FAM3A promoter activity and FAM3A inhibits adipocyte differentiation.
    Title: Transcriptional regulation analysis of FAM3A gene and its effect on adipocyte differentiation.
  6. In the present study, we report a putative human homologue of the antimicrobial Drosophila-derived drosomycin, designated drosomycin-like defensin (DLD), with specific antifungal activity.
    Title: Drosomycin-like defensin, a human homologue of Drosophila melanogaster drosomycin with antifungal activity.
  7. FAM3A plays crucial roles in the regulation of glucose and lipid metabolism in the liver, where it activates the PI3K-Akt signaling pathway by way of a Ca(2+) /CaM-dependent mechanism
    Title: FAM3A activates PI3K p110α/Akt signaling to ameliorate hepatic gluconeogenesis and lipogenesis.
  8. Upregulation of FAM3A by PPARgamma activation is correlated with increased pAkt level in liver cells
    Title: FAM3A is a target gene of peroxisome proliferator-activated receptor gamma.
  9. Expressed prominently in the vascular endothelium, particularly capillaries, also in islets of Langerhans.
    Title: Cloning, expression, and initial characterization of a novel cytokine-like gene family.
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
Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.
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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in antifungal humoral response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of antifungal innate immune response IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein FAM3A
Names
cytokine-like protein 2-19
family with sequence similarity 3 member A

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.

Genomic

  1. NG_016401.2 RefSeqGene

    Range
    5121..15182
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001171132.3 → NP_001164603.1  protein FAM3A isoform 1 precursor

    See identical proteins and their annotated locations for NP_001164603.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2 and 6 encode the same isoform (1).
    Source sequence(s)
    AL539139, AW612420, BC008912, BM457676, X87193
    Consensus CDS
    CCDS35453.1
    UniProtKB/Swiss-Prot
    A6QRH6, B2RBI7, B4DFI8, D3DWX4, P98173, Q5HY76, Q96H51
    Related
    ENSP00000352955.5, ENST00000359889.9
    Conserved Domains (1) summary
    cd13940
    Location:55 → 224
    ILEI_FAM3C; Interleukin-like EMT inducer

  2. NM_001171133.3 → NP_001164604.1  protein FAM3A isoform 2

    See identical proteins and their annotated locations for NP_001164604.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AL539139, AW612420, BC008912, BM457676, X87193
    Consensus CDS
    CCDS55542.1
    UniProtKB/Swiss-Prot
    P98173
    Related
    ENSP00000377202.1, ENST00000393572.5
    Conserved Domains (1) summary
    cd13940
    Location:17 → 186
    ILEI_FAM3C; Interleukin-like EMT inducer

  3. NM_001171134.3 → NP_001164605.1  protein FAM3A isoform 3

    See identical proteins and their annotated locations for NP_001164605.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AK314682, AL539139, AW612420, BM457676, X87193
    Consensus CDS
    CCDS55543.1
    UniProtKB/Swiss-Prot
    P98173
    Related
    ENSP00000393086.2, ENST00000419205.5
    Conserved Domains (1) summary
    cd13940
    Location:55 → 207
    ILEI_FAM3C; Interleukin-like EMT inducer

  4. NM_001282311.2 → NP_001269240.1  protein FAM3A isoform 4

    See identical proteins and their annotated locations for NP_001269240.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate exon in its 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) has a longer and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AL539139, AW612420, BC002934, BM457676, X87193
    Consensus CDS
    CCDS76060.1
    UniProtKB/TrEMBL
    D3DWX8
    Related
    ENSP00000320521.7, ENST00000322269.10
    Conserved Domains (1) summary
    cd13940
    Location:69 → 238
    ILEI_FAM3C; Interleukin-like EMT inducer

  5. NM_001282312.2 → NP_001269241.1  protein FAM3A isoform 1 precursor

    See identical proteins and their annotated locations for NP_001269241.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1. Variants 1, 2 and 6 encode the same isoform (1).
    Source sequence(s)
    AL539139, AW612420, BC008912, BM457676, X87193
    Consensus CDS
    CCDS35453.1
    UniProtKB/Swiss-Prot
    A6QRH6, B2RBI7, B4DFI8, D3DWX4, P98173, Q5HY76, Q96H51
    Related
    ENSP00000358657.1, ENST00000369643.5
    Conserved Domains (1) summary
    cd13940
    Location:55 → 224
    ILEI_FAM3C; Interleukin-like EMT inducer

  6. NM_001363822.2 → NP_001350751.1  protein FAM3A isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC244090
    Consensus CDS
    CCDS87800.1
    UniProtKB/TrEMBL
    Q5HY75
    Related
    ENSP00000358655.3, ENST00000369641.7
    Conserved Domains (1) summary
    cd13940
    Location:55 → 231
    ILEI_FAM3C; Interleukin-like EMT inducer

  7. NM_021806.4 → NP_068578.2  protein FAM3A isoform 1 precursor

    See identical proteins and their annotated locations for NP_068578.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform (1). Variants 1, 2 and 6 encode the same isoform (1).
    Source sequence(s)
    AK314682, AL539139, AW612420, BM457676, X87193
    Consensus CDS
    CCDS35453.1
    UniProtKB/Swiss-Prot
    A6QRH6, B2RBI7, B4DFI8, D3DWX4, P98173, Q5HY76, Q96H51
    Related
    ENSP00000416146.2, ENST00000447601.7
    Conserved Domains (1) summary
    cd13940
    Location:55 → 224
    ILEI_FAM3C; Interleukin-like EMT inducer

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    154506171..154516232 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005277879.5 → XP_005277936.1  protein FAM3A isoform X4

    See identical proteins and their annotated locations for XP_005277936.1

    UniProtKB/Swiss-Prot
    P98173
    Conserved Domains (1) summary
    cd13940
    Location:55 → 207
    ILEI_FAM3C; Interleukin-like EMT inducer

  2. XM_006724832.4 → XP_006724895.1  protein FAM3A isoform X2

    See identical proteins and their annotated locations for XP_006724895.1

    Conserved Domains (1) summary
    cd13940
    Location:55 → 232
    ILEI_FAM3C; Interleukin-like EMT inducer

  3. XM_024452418.2 → XP_024308186.1  protein FAM3A isoform X3

    Conserved Domains (1) summary
    cd13940
    Location:69 → 221
    ILEI_FAM3C; Interleukin-like EMT inducer

  4. XM_024452416.2 → XP_024308184.1  protein FAM3A isoform X1

    Conserved Domains (1) summary
    cd13940
    Location:69 → 245
    ILEI_FAM3C; Interleukin-like EMT inducer

  5. XM_047442293.1 → XP_047298249.1  protein FAM3A isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152742672..152752723 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327475.1 → XP_054183450.1  protein FAM3A isoform X4

  2. XM_054327473.1 → XP_054183448.1  protein FAM3A isoform X2

  3. XM_054327474.1 → XP_054183449.1  protein FAM3A isoform X3

  4. XM_054327472.1 → XP_054183447.1  protein FAM3A isoform X1

  5. XM_054327476.1 → XP_054183451.1  protein FAM3A isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P98173.2 GenPept UniProtKB/Swiss-Prot:P98173

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