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    FAM20A FAM20A golgi associated secretory pathway pseudokinase [ Homo sapiens (human) ]

    Gene ID: 54757, updated on 10-Dec-2024

    Summary

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    Official Symbol
    FAM20Aprovided by HGNC
    Official Full Name
    FAM20A golgi associated secretory pathway pseudokinaseprovided by HGNC
    Primary source
    HGNC:HGNC:23015
    See related
    Ensembl:ENSG00000108950 MIM:611062; AllianceGenome:HGNC:23015
    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
    AI1G; AIGFS; FP2747
    Summary
    This locus encodes a protein that is likely secreted and may function in hematopoiesis. A mutation at this locus has been associated with amelogenesis imperfecta and gingival hyperplasia syndrome. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Aug 2011]
    Expression
    Broad expression in salivary gland (RPKM 7.2), liver (RPKM 6.1) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FAM20A in Genome Data Viewer
    Location:
    17q24.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (68535116..68601367, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (69411970..69478232, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (66531257..66597508, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene arylsulfatase G Neighboring gene tRNA-undetermined (NNN) 5-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66409262-66409920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66409921-66410577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:66432181-66432681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8900 Neighboring gene protein kinase cAMP-dependent type I regulatory subunit alpha Neighboring gene ReSE screen-validated silencer GRCh37_chr17:66453793-66454079 Neighboring gene microRNA 635 Neighboring gene WD repeat domain, phosphoinositide interacting 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8902 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:66494688-66494871 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66508045-66508618 Neighboring gene Sharpr-MPRA regulatory region 15560 Neighboring gene Sharpr-MPRA regulatory region 13674 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66627729-66628228 Neighboring gene long intergenic non-protein coding RNA 1482 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66682485-66682986 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66682987-66683486 Neighboring gene uncharacterized LOC124904049

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. FAM20A is a golgi-localized Type II transmembrane protein. Siddiqui MF, et al. Sci Rep, 2024 Mar 18. PMID 38499693, Free PMC Article
    2. FAM20A mutations associated with enamel renal syndrome. Wang SK, et al. J Dent Res, 2014 Jan. PMID 24196488, Free PMC Article
    3. Enamel-renal-gingival syndrome and FAM20A mutations. Kantaputra PN, et al. Am J Med Genet A, 2014 Jan. PMID 24259279
    4. Periodontal disease and FAM20A mutations. Kantaputra PN, et al. J Hum Genet, 2017 Jul. PMID 28298625
    5. Nephrocalcinosis in Amelogenesis Imperfecta Caused by the FAM20A Mutation. Koruyucu M, et al. Nephron, 2018. PMID 29439260

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FAM20A-Associated Amelogenesis Imperfecta: Gene Variants with Functional Verification and Histological Features.
      Title: FAM20A-Associated Amelogenesis Imperfecta: Gene Variants with Functional Verification and Histological Features.
    2. FAM20A is a golgi-localized Type II transmembrane protein.
      Title: FAM20A is a golgi-localized Type II transmembrane protein.
    3. Deep dental phenotyping and a novel FAM20A variant in patients with amelogenesis imperfecta type IG.
      Title: Deep dental phenotyping and a novel FAM20A variant in patients with amelogenesis imperfecta type IG.
    4. FAM20A mutations and transcriptome analyses of dental pulp tissues of enamel renal syndrome.
      Title: FAM20A mutations and transcriptome analyses of dental pulp tissues of enamel renal syndrome.
    5. Two new families with enamel renal syndrome: A novel FAM20A gene mutation and review of literature.
      Title: Two new families with enamel renal syndrome: A novel FAM20A gene mutation and review of literature.
    6. Whole exome sequencing (WES) identified that Pt-1 was heterozygous for FAM20A, c.758A > G (p.Tyr253Cys), inherited from her father. The mutation on maternal allele was not detected by WES. Pt-2 possessed compound heterozygous mutations, c.1248dupG (p.Phe417Valfs*7); c.1081C > T (p.Arg361Cys) in FAM20A.
      Title: Four novel mutations of FAM20A in amelogenesis imperfecta type IG and review of literature for its genotype and phenotype spectra.
    7. Here we report the largest series of patients with Enamel renal syndrome in a same population, and describe, for the first time, a founder mutation for FAM20A.
      Title: Enamel renal syndrome: A novel homozygous FAM20A founder mutation in 5 new Brazilian families.
    8. Mutations in LAMB3 and FAM20A were found in 3 Turkish families with Amelogenesis imperfecta
      Title: Candidate gene sequencing reveals mutations causing hypoplastic amelogenesis imperfecta.
    9. Recessive FAM20A mutations can cause nephrocalcinosis in addition to the oral phenotype
      Title: Nephrocalcinosis in Amelogenesis Imperfecta Caused by the FAM20A Mutation.
    10. Physicochemical analysis of human pulpal mineralization secondary to FAM20A mutations.
      Title: Physicochemical analysis of human pulpal mineralization secondary to FAM20A mutations.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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

    Associated conditions

    Description Tests
    Amelogenesis imperfecta type 1G
    MedGen: C2931783 OMIM: 204690 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    • DKFZp434F2322

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables phosphotransferase activity, alcohol group as acceptor IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein serine/threonine kinase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein serine/threonine kinase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT enables protein serine/threonine kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biomineral tissue development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in calcium ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in enamel mineralization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in enamel mineralization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of protein phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in response to bacterium IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tooth eruption IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    colocalizes_with Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pseudokinase FAM20A
    Names
    family with sequence similarity 20, member A
    protein FAM20A

    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_029809.1 RefSeqGene

      Range
      4588..70839
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243746.2 → NP_001230675.1  pseudokinase FAM20A isoform b

      See identical proteins and their annotated locations for NP_001230675.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon at its 5' end and uses a downstream start codon, compared to variant 1. The encoded protein (isoform b) has a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AC079210, AK298071, AL133105, AY358197, BC036222
      UniProtKB/TrEMBL
      B7Z4Y3
      Conserved Domains (1) summary
      cd10469
      Location:168 → 384
      FAM20A_C; C-terminal putative kinase domain of FAM20A

    2. NM_017565.4 → NP_060035.2  pseudokinase FAM20A isoform a precursor

      See identical proteins and their annotated locations for NP_060035.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC079210, AL133105, AY358197, BC036222, BC136686, CB530015, N64017
      Consensus CDS
      CCDS11679.1
      UniProtKB/Swiss-Prot
      B2RN47, B2RN49, Q96MK3, Q9UF95
      UniProtKB/TrEMBL
      L8B8N7
      Related
      ENSP00000468308.1, ENST00000592554.2
      Conserved Domains (1) summary
      cd10469
      Location:306 → 522
      FAM20A_C; C-terminal putative kinase domain of FAM20A

    RNA

    1. NR_027751.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has multiple differences compared to variant 1. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because there is uncertainty about the protein-coding capacity of the transcript.
      Source sequence(s)
      AC079210, AL133105, BC036222, CB530015, DB057818, N64017
      Related
      ENST00000226094.9

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      68535116..68601367 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006721959.4 → XP_006722022.1  pseudokinase FAM20A isoform X1

      See identical proteins and their annotated locations for XP_006722022.1

      UniProtKB/TrEMBL
      B7Z4Y3
      Conserved Domains (1) summary
      cd10469
      Location:168 → 384
      FAM20A_C; C-terminal putative kinase domain of FAM20A

    2. XM_047436319.1 → XP_047292275.1  pseudokinase FAM20A isoform X3

    3. XM_017024781.3 → XP_016880270.1  pseudokinase FAM20A isoform X2

      Conserved Domains (1) summary
      cl05973
      Location:306 → 373
      FAM20_C_like; C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins

    4. XM_011524918.4 → XP_011523220.1  pseudokinase FAM20A isoform X4

      Conserved Domains (1) summary
      cl05973
      Location:306 → 370
      FAM20_C_like; C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins

    RNA

    1. XR_002958041.2 RNA Sequence

    2. XR_934487.4 RNA Sequence

    3. XR_001752543.3 RNA Sequence

    4. XR_429905.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      69411970..69478232 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316546.1 → XP_054172521.1  pseudokinase FAM20A isoform X1

      UniProtKB/TrEMBL
      B7Z4Y3

    2. XM_054316548.1 → XP_054172523.1  pseudokinase FAM20A isoform X3

    3. XM_054316547.1 → XP_054172522.1  pseudokinase FAM20A isoform X2

    4. XM_054316549.1 → XP_054172524.1  pseudokinase FAM20A isoform X4

    RNA

    1. XR_008484843.1 RNA Sequence

    2. XR_008484844.1 RNA Sequence

    3. XR_008484845.1 RNA Sequence

    4. XR_008484846.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96MK3.4 GenPept UniProtKB/Swiss-Prot:Q96MK3

    Gene LinkOut

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

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