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

Summary

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: mouse all
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Genomic context

Location:: 6q25.3

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (158109519..158168262, complement)
110	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_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Severe neonatal MEGDHEL syndrome with a homozygous truncating mutation in SERAC1.
Title: Severe neonatal MEGDHEL syndrome with a homozygous truncating mutation in SERAC1.
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.
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.
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.
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.
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.
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.
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.
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

Associated conditions

Description	Tests
3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome MedGen: C4040739 OMIM: 614739 GeneReviews: SERAC1 Deficiency	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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S1120E (e-PCR)
- UniSTS:151084

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

D1S1423 (e-PCR)
- UniSTS:149619

D1S1425 (e-PCR)
- UniSTS:149621

RH77847 (e-PCR)
- UniSTS:42882

D6S363 (e-PCR)
- UniSTS:148107

D11S3114 (e-PCR)
- UniSTS:152207

RH76368 (e-PCR)
- UniSTS:92577

AFM309yb9 (e-PCR)
- UniSTS:50154

Homology

Homologs of the SERAC1 gene: The SERAC1 gene is conserved in Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, rice, and frog.
Orthologs from Annotation Pipeline: 505 organisms have orthologs with human gene SERAC1
Orthologs

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	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

NG_032889.1 RefSeqGene

Range

5019..63762

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Q6PKF3, Q96JX3

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

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: Homo sapiens Annotation Release 110 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

158109519..158168262 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006715586.4 → XP_006715649.1 protein SERAC1 isoform X3

See identical proteins and their annotated locations for XP_006715649.1

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
XM_047419421.1 → XP_047275377.1 protein SERAC1 isoform X2
XM_024446573.2 → XP_024302341.1 protein SERAC1 isoform X1

UniProtKB/Swiss-Prot

Q6PKF3
XM_011536198.4 → XP_011534500.1 protein SERAC1 isoform X3

See identical proteins and their annotated locations for XP_011534500.1

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