hmgcs1 3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble) [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hmgcs1provided by ZNC
Official Full Name: 3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)provided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-1042
See related: Ensembl:ENSDARG00000103025 AllianceGenome:ZFIN:ZDB-GENE-040426-1042
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: zgc:56481
Summary: Predicted to enable hydroxymethylglutaryl-CoA synthase activity. Acts upstream of or within several processes, including embryonic viscerocranium morphogenesis; erythrocyte development; and oligodendrocyte development. Is expressed in several structures, including digestive system; immature eye; nervous system; pectoral fin musculature; and yolk syncytial layer. Human ortholog(s) of this gene implicated in HMG-CoA synthase 2 deficiency. Orthologous to several human genes including HMGCS1 (3-hydroxy-3-methylglutaryl-CoA synthase 1). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs: all
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Genomic context

Location:: chromosome: 10

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2025_04	current	GRCz12tu (GCF_049306965.1)	10	NC_133185.1 (6490147..6513905)
RS_2024_08	previous assembly	GRCz11 (GCF_000002035.6)	10	NC_007121.7 (6010652..6034410)

Chromosome 10 - NC_133185.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mutation of hmgcs1 resulted in a decrease in the number of mature RBCs, which coincides with reduced gata1a expression.
Title: Mutations in the zebrafish hmgcs1 gene reveal a novel function for isoprenoids during red blood cell development.
Mutation of hmgcs1 had no effect on Shh signaling at 2 and 3 days post fertilization (dpf), but did result in a decrease in the expression of gli1, a known Shh target gene, at 4 dpf, after morphological deficits in craniofacial development and chondrocyte differentiation were observed in hmgcs1 mutants.
Title: Functional analysis of the zebrafish ortholog of HMGCS1 reveals independent functions for cholesterol and isoprenoids in craniofacial development.
This study identified a mutation of hmgcs1, coding for Hmg-CoA synthase 1, which caused OPCs to migrate past their target axons and interfered with myelin gene expression.
Title: Mutation of 3-hydroxy-3-methylglutaryl CoA synthase I reveals requirements for isoprenoid and cholesterol synthesis in oligodendrocyte migration arrest, axon wrapping, and myelin gene expression.

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General gene information

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Markers

fj79g05.y1 (e-PCR)
- UniSTS:199937

fk73h03.x1 (e-PCR)
- UniSTS:201489

fb62h09.y1 (e-PCR)
- UniSTS:190897

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables acyltransferase activity	IEA Inferred from Electronic Annotation more info
enables hydroxymethylglutaryl-CoA synthase activity	IBA Inferred from Biological aspect of Ancestor more info
enables hydroxymethylglutaryl-CoA synthase activity	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in acetyl-CoA metabolic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within acetyl-CoA metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cholesterol biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cholesterol metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within erythrocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in farnesyl diphosphate biosynthetic process, mevalonate pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within farnesyl diphosphate biosynthetic process, mevalonate pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within isoprenoid biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lipid metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural crest cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within oligodendrocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within steroid biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within steroid metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sterol biosynthetic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cellular_component	ND No biological Data available more info

General protein information

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Preferred Names: hydroxymethylglutaryl-CoA synthase, cytoplasmic

Names: 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)

NP_957379.2

EC 2.3.3.10

XP_005155548.1

EC 2.3.3.10

XP_073769782.1

EC 2.3.3.10

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)

NM_201085.2 → NP_957379.2 hydroxymethylglutaryl-CoA synthase, cytoplasmic

Status: VALIDATED

Source sequence(s)

JBMGRA010000010

UniProtKB/TrEMBL

A0A8M1PIL7

Conserved Domains (3) summary

TIGR01833
Location:20 → 477

HMG-CoA-S_euk; 3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic clade

pfam01154
Location:23 → 193

HMG_CoA_synt_N; Hydroxymethylglutaryl-coenzyme A synthase N terminal

pfam08540
Location:194 → 477

HMG_CoA_synt_C; Hydroxymethylglutaryl-coenzyme A synthase C terminal

RefSeqs of Annotated Genomes: GCF_049306965.1-RS_2025_04

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

Reference GRCz12tu Primary Assembly

Genomic

NC_133185.1 Reference GRCz12tu Primary Assembly

Range

6490147..6513905

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005155491.4 → XP_005155548.1 hydroxymethylglutaryl-CoA synthase, cytoplasmic isoform X1

UniProtKB/TrEMBL

A0A0R4IQG1, A0A8M2B251, A0AC58GJ33

Related

ENSDARP00000145051.1, ENSDART00000190025.1

Conserved Domains (3) summary

TIGR01833
Location:13 → 470

HMG-CoA-S_euk; 3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic clade

pfam01154
Location:16 → 186

HMG_CoA_synt_N; Hydroxymethylglutaryl-coenzyme A synthase N terminal

pfam08540
Location:187 → 470

HMG_CoA_synt_C; Hydroxymethylglutaryl-coenzyme A synthase C terminal
XM_073913681.1 → XP_073769782.1 hydroxymethylglutaryl-CoA synthase, cytoplasmic isoform X1

UniProtKB/TrEMBL

A0A0R4IQG1, A0A8M2B251, A0AC58GJ33