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SERAC1 serine active site containing 1 [ Homo sapiens (human) ]

Gene ID: 84947, updated on 11-Apr-2024

Summary

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Official Symbol
SERAC1provided by HGNC
Official Full Name
serine active site containing 1provided by HGNC
Primary source
HGNC:HGNC:21061
See related
Ensembl:ENSG00000122335 MIM:614725; AllianceGenome:HGNC:21061
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
Summary
The protein encoded by this gene is a phosphatidylglycerol remodeling protein found at the interface of mitochondria and endoplasmic reticula, where it mediates phospholipid exchange. The encoded protein plays a major role in mitochondrial function and intracellular cholesterol trafficking. Defects in this gene are a cause of 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome (MEGDEL). Two transcript variants, one protein-coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Aug 2012]
Expression
Ubiquitous expression in testis (RPKM 4.2), adrenal (RPKM 3.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
6q25.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (158109519..158168262, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159355719..159413646, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (158530551..158589294, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene sorting nexin 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17730 Neighboring gene RNA, U6 small nuclear 786, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr6.5510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158394739-158395292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402145-158402660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402661-158403176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158420467-158420966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447101-158447788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447789-158448476 Neighboring gene SYNJ2 intronic transcript 1 Neighboring gene Sharpr-MPRA regulatory region 12557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158458586-158459280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158461967-158462502 Neighboring gene synaptojanin 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158470498-158471112 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:158490014-158491213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492197-158492760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492761-158493322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158516915-158517415 Neighboring gene MPRA-validated peak6269 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158604741-158605243 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158604236-158604740 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:158615403-158616003 Neighboring gene general transcription factor IIH subunit 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:158653118-158653990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25349 Neighboring gene signal recognition particle 72 pseudogene 2 Neighboring gene TUB like protein 4

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. First description of the MEGDEHL syndrome in the Tunisian population via whole-exome sequencing: Novel nonsense mutation in SERAC1 gene. Felhi R, et al. Int J Dev Neurosci, 2022 Dec. PMID 35943861
  2. Severe neonatal MEGDHEL syndrome with a homozygous truncating mutation in SERAC1. Fellman V, et al. Biochim Biophys Acta Mol Basis Dis, 2022 Jan 1. PMID 34751152
  3. Progressive deafness-dystonia due to SERAC1 mutations: A study of 67 cases. Maas RR, et al. Ann Neurol, 2017 Dec. PMID 29205472, Free PMC Article
  4. SERAC1 deficiency causes complicated HSP: evidence from a novel splice mutation in a large family. Roeben B, et al. J Med Genet, 2018 Jan. PMID 28916646
  5. Novel mutations in SERAC1 gene in two Indian patients presenting with dystonia and intellectual disability. Radha Rama Devi A, et al. Eur J Med Genet, 2018 Feb. PMID 28778788

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. First description of the MEGDEHL syndrome in the Tunisian population via whole-exome sequencing: Novel nonsense mutation in SERAC1 gene.
    Title: First description of the MEGDEHL syndrome in the Tunisian population via whole-exome sequencing: Novel nonsense mutation in SERAC1 gene.
  2. Severe neonatal MEGDHEL syndrome with a homozygous truncating mutation in SERAC1.
    Title: Severe neonatal MEGDHEL syndrome with a homozygous truncating mutation in SERAC1.
  3. Our study indicates that the cochlear CHI is a phenotypic feature of the RRM2B and SERAC1 related defects.
    Title: Congenital cochlear deafness in mitochondrial diseases related to RRM2B and SERAC1 gene defects. A study of the mitochondrial patients of the CMHI hospital in Warsaw, Poland.
  4. Two novel SERAC1 mutations were identified in two cases of dystonia, 3-methylglutaconic aciduria and intellectual disability syndrome.
    Title: Novel mutations in SERAC1 gene in two Indian patients presenting with dystonia and intellectual disability.
  5. mutations in the phosphatidylglycerol remodelling enzyme SERAC1 can cause juvenile-onset complicated hereditary spastic paraplegia (cHSP) clusters
    Title: SERAC1 deficiency causes complicated HSP: evidence from a novel splice mutation in a large family.
  6. Several different SERAC1 variants were identified from individuals with Deafness-Dystonia syndrome.
    Title: Progressive deafness-dystonia due to SERAC1 mutations: A study of 67 cases.
  7. Here we report two new Turkish sibling patients affected with MEGDEL syndrome due to SERAC1 gene mutation.
    Title: Two Turkish siblings with MEGDEL syndrome due to novel SERAC1 gene mutation.
  8. Infantile mitochondrial hepatopathy is a cardinal feature of MEGDEL syndrome (3-methylglutaconic aciduria type IV with sensorineural deafness, encephalopathy and Leigh-like syndrome) caused by novel mutations in SERAC1.
    Title: Infantile mitochondrial hepatopathy is a cardinal feature of MEGDEL syndrome (3-methylglutaconic aciduria type IV with sensorineural deafness, encephalopathy and Leigh-like syndrome) caused by novel mutations in SERAC1.
  9. During the course of this project a parallel study identified mutations in SERAC1 as the genetic cause of the disease in 15 patients with MEGDEL syndrome, which was compatible with the clinical and biochemical phenotypes of the patient described here.
    Title: Exome sequencing identifies a new mutation in SERAC1 in a patient with 3-methylglutaconic aciduria.
  10. Data identify SERAC1 as a key player in the phosphatidylglycerol remodeling that is essential for both mitochondrial function and intracellular cholesterol trafficking.
    Title: Mutations in the phospholipid remodeling gene SERAC1 impair mitochondrial function and intracellular cholesterol trafficking and cause dystonia and deafness.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ14917, FLJ30544

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in extracellular matrix organization IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular cholesterol transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in phosphatidylglycerol acyl-chain remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in phospholipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular matrix IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondria-associated endoplasmic reticulum membrane contact site IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
protein SERAC1
Names
serine active site-containing protein 1

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_032889.1 RefSeqGene

    Range
    5019..63762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_032861.4 → NP_116250.3  protein SERAC1

    See identical proteins and their annotated locations for NP_116250.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and is the protein-coding variant.
    Source sequence(s)
    AK027823, BC001705
    Consensus CDS
    CCDS5255.1
    UniProtKB/Swiss-Prot
    Q49AT1, Q5VTX3, Q6PKF3, Q96JX3
    UniProtKB/TrEMBL
    A0A2R8Y3S0
    Related
    ENSP00000496731.1, ENST00000647468.2
    Conserved Domains (2) summary
    COG0596
    Location:386 → 592
    MhpC; Pimeloyl-ACP methyl ester carboxylesterase [Coenzyme transport and metabolism, General function prediction only]
    cl21494
    Location:396 → 540
    Abhydrolase; alpha/beta hydrolases

RNA

  1. NR_073096.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate internal exons and has an alternate 3' exon structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL590703, BC048335, DA232092
    Related
    ENST00000606965.5

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    158109519..158168262 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715586.4 → XP_006715649.1  protein SERAC1 isoform X3

    See identical proteins and their annotated locations for XP_006715649.1

    UniProtKB/TrEMBL
    A0A2R8Y511
    Related
    ENSP00000493723.1, ENST00000646208.1
    Conserved Domains (2) summary
    COG0596
    Location:316 → 522
    MhpC; Pimeloyl-ACP methyl ester carboxylesterase [Coenzyme transport and metabolism, General function prediction only]
    cl21494
    Location:326 → 470
    Abhydrolase; alpha/beta hydrolases

  2. XM_047419421.1 → XP_047275377.1  protein SERAC1 isoform X2

  3. XM_024446573.2 → XP_024302341.1  protein SERAC1 isoform X1

    UniProtKB/Swiss-Prot
    Q49AT1, Q5VTX3, Q6PKF3, Q96JX3
    UniProtKB/TrEMBL
    A0A2R8Y3S0

  4. XM_011536198.4 → XP_011534500.1  protein SERAC1 isoform X3

    See identical proteins and their annotated locations for XP_011534500.1

    UniProtKB/TrEMBL
    A0A2R8Y511
    Conserved Domains (2) summary
    COG0596
    Location:316 → 522
    MhpC; Pimeloyl-ACP methyl ester carboxylesterase [Coenzyme transport and metabolism, General function prediction only]
    cl21494
    Location:326 → 470
    Abhydrolase; alpha/beta hydrolases

RNA

  1. XR_007059349.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    159355719..159413646 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356600.1 → XP_054212575.1  protein SERAC1 isoform X3

  2. XM_054356599.1 → XP_054212574.1  protein SERAC1 isoform X2

  3. XM_054356598.1 → XP_054212573.1  protein SERAC1 isoform X1

    UniProtKB/Swiss-Prot
    Q49AT1, Q5VTX3, Q6PKF3, Q96JX3

  4. XM_054356601.1 → XP_054212576.1  protein SERAC1 isoform X3

RNA

  1. XR_008487454.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96JX3.1 GenPept UniProtKB/Swiss-Prot:Q96JX3

Gene LinkOut

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