Scd1 Gene Detail

Summary

• Symbol
  Scd1
• Name
  stearoyl-Coenzyme A desaturase 1
• Synonyms
  SCD, Scd-1, stearoyl-CoA desaturase

• Feature Type
  protein coding gene
• IDs
  MGI:98239
  NCBI Gene: 20249
• Alliance
  gene page
• Transcription Start Sites
  87 TSS
• Candidate for QTL
  2 QTL

Location &
Maps

• Sequence Map
  Chr19:44382889-44396148 bp, - strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 19, 37.98 cM
• Mapping Data
  25 experiments

Strain
Comparison

• SNPs within 2kb
  442 from dbSNP Build 142
• Strain Annotations
  18
• RFLP
  4

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_98239	protein coding gene	Chr19:44382889-44396318 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0025170	protein coding gene	Chr19:43875426-43890076 (-)
A/J	MGP_AJ_G0025147	protein coding gene	Chr19:41775309-41788567 (-)
AKR/J	MGP_AKRJ_G0025115	protein coding gene	Chr19:43118810-43133816 (-)
BALB/cJ	MGP_BALBcJ_G0025141	protein coding gene	Chr19:41825984-41839242 (-)
C3H/HeJ	MGP_C3HHeJ_G0024901	protein coding gene	Chr19:43277617-43290867 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0025584	protein coding gene	Chr19:44956723-44969981 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022998	protein coding gene	Chr19:41056735-41069912 (-)
CAST/EiJ	MGP_CASTEiJ_G0024366	protein coding gene	Chr19:42982922-42997663 (-)
CBA/J	MGP_CBAJ_G0024881	protein coding gene	Chr19:47220986-47234248 (-)
DBA/2J	MGP_DBA2J_G0025013	protein coding gene	Chr19:41591584-41604985 (-)
FVB/NJ	MGP_FVBNJ_G0024974	protein coding gene	Chr19:41365523-41378812 (-)
LP/J	MGP_LPJ_G0025099	protein coding gene	Chr19:43818252-43832410 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025005	protein coding gene	Chr19:46666067-46679325 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025642	protein coding gene	Chr19:43185878-43200194 (-)
PWK/PhJ	MGP_PWKPhJ_G0024115	protein coding gene	Chr19:41493577-41507584 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0023919	protein coding gene	Chr19:41902401-41916077 (-)
WSB/EiJ	MGP_WSBEiJ_G0024436	protein coding gene	Chr19:43315376-43329083 (-)

Homology

• Human Ortholog
  SCD, stearoyl-CoA desaturase

• Vertebrate Orthologs
  4

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  SCD, stearoyl-CoA desaturase
  
• Synonyms
  FADS5, hSCD1, MSTP008, SCD1, SCDOS
• Links
  HGNC:10571

  NCBI Gene ID: 6319

  neXtProt AC: NX_O00767

  UniProt: O00767

  
  
• Chr Location
  10q24.31; chr10:100347233-100364826 (+)  GRCh38

---

• MGI Vertebrate Homology
  Scd1 stringent orthology
  1 human;1 mouse;1 rat;2 zebrafish
  
• HCOP
  vertebrate homology predictions: SCD
• Gene Tree
  Scd1
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  95 phenotypes from 8 alleles in 10 genetic backgrounds
  17 phenotypes from multigenic genotypes
  2 images
  108 phenotype references
  

• All Mutations and Alleles
  18
• Chemically induced (ENU)
  1
• Endonuclease-mediated
  4
• Gene trapped
  3
• Spontaneous
  4
• Targeted
  4
• Transgenic
  2
• Genomic Mutations
  1 involving Scd1
• Incidental Mutations
  APF
• Find Mice (IMSR)
  24 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Homozygotes for targeted and spontaneous mutations exhibit alopecia, scaly skin, sebaceous gland hypoplasia, impaired ocular lubrication and synthesis and storage of triglycerides, higher lipid oxidation, reduced growth, and lower fertility in females.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  47
• GO References
  18

Expression

• Assay Results
  896
• Tissues
  121
• cDNA Data
  32
• Literature Summary
  50

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase scd
  ZFIN scd, scdb

Sequences &
Gene Models

• All Sequences
  56
• RefSeq
  2
• UniProt
  4
• CCDS
  CCDS29850.1

• Ensembl
  ENSMUSG00000037071 (Evidence)
• NCBI Gene
  20249

Representative Sequences			Length	Strain/Species
genomic	20249	NCBI Gene Model | MGI Sequence Detail	13260	C57BL/6J
transcript	NM_009127	RefSeq | MGI Sequence Detail	4844	ZRU/MplStud
polypeptide	P13516	UniProt | EBI | MGI Sequence Detail	355	Not Applicable

Protein
Information

• UniProt
  4 Sequences
• Protein Ontology
  PR:000015921 acyl-CoA desaturase 1
  (term hierarchy)
• PDB
  4YMK, 6WF2
• EC
  1.14.19.1
• InterPro Domains
  IPR015876 Acyl-CoA desaturase
  IPR005804 Fatty acid desaturase domain
  IPR001522 Fatty acid desaturase type 1, conserved site

Molecular
Reagents

• All nucleic 54

  Genomic 7

  cDNA 35

  Primer pair 11

  Other 1

  
  

  Microarray probesets 9

Other
Accession IDs

MGD-MRK-1014, MGD-MRK-14305, MGD-MRK-14307, MGI:2147455, MGI:2147495, MGI:87858

References

• Summaries
  All 257

  Developmental Gene Expression 50

  Gene Ontology 18

  Phenotypes 108
• Earliest
  J:13143 Gates AH, et al., Hereditary absence of sebaceous glands in the mouse. Science. 1965;148:1471-1473
• Latest
  J:354192 He H, et al., PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function. Nat Commun. 2024 Sep 16;15(1):8112

TSS for Scd1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr159526	Chr19:44397203-44397215 (-)	-1,061 bp
Tssr159525	Chr19:44397173-44397196 (-)	-1,037 bp
Tssr159524	Chr19:44396322-44396340 (-)	-183 bp
Tssr159523	Chr19:44396270-44396316 (-)	-145 bp
Tssr159522	Chr19:44396248-44396261 (-)	-107 bp
Tssr159521	Chr19:44396142-44396151 (-)	1 bp
Tssr159520	Chr19:44396098-44396107 (-)	45 bp
Tssr159519	Chr19:44396049-44396062 (-)	92 bp
Tssr5529	Chr19:44396021-44396038 (-)	118 bp
Tssr159518	Chr19:44395992-44396008 (-)	148 bp
Tssr5528	Chr19:44395983-44395987 (-)	163 bp
Tssr5527	Chr19:44395954-44395957 (-)	192 bp
Tssr5526	Chr19:44395944-44395947 (-)	202 bp
Tssr159517	Chr19:44395928-44395937 (-)	215 bp
Tssr5525	Chr19:44395857-44395914 (-)	262 bp
Tssr159516	Chr19:44395157-44395207 (-)	966 bp
Tssr159515	Chr19:44395070-44395091 (-)	1,067 bp
Tssr159514	Chr19:44395064-44395069 (-)	1,081 bp
Tssr159513	Chr19:44394969-44395021 (-)	1,153 bp
Tssr159512	Chr19:44392021-44392034 (-)	4,120 bp
Tssr159511	Chr19:44391716-44391738 (-)	4,421 bp
Tssr159510	Chr19:44391680-44391698 (-)	4,459 bp
Tssr159509	Chr19:44391667-44391677 (-)	4,476 bp
Tssr159508	Chr19:44388711-44388747 (-)	7,419 bp
Tssr159507	Chr19:44388625-44388674 (-)	7,498 bp
Tssr159506	Chr19:44388604-44388621 (-)	7,535 bp
Tssr159505	Chr19:44386532-44386557 (-)	9,603 bp
Tssr159504	Chr19:44386419-44386451 (-)	9,713 bp
Tssr159503	Chr19:44386340-44386386 (-)	9,785 bp
Tssr159502	Chr19:44386327-44386334 (-)	9,817 bp
Tssr159501	Chr19:44386291-44386323 (-)	9,841 bp
Tssr159500	Chr19:44386276-44386287 (-)	9,866 bp
Tssr159499	Chr19:44386245-44386273 (-)	9,889 bp
Tssr159498	Chr19:44386215-44386221 (-)	9,930 bp
Tssr159497	Chr19:44386203-44386210 (-)	9,941 bp
Tssr159496	Chr19:44386190-44386200 (-)	9,953 bp
Tssr159495	Chr19:44386120-44386180 (-)	9,998 bp
Tssr159494	Chr19:44386002-44386031 (-)	10,131 bp
Tssr159493	Chr19:44385982-44385993 (-)	10,160 bp
Tssr159492	Chr19:44385956-44385969 (-)	10,185 bp
Tssr159491	Chr19:44385905-44385926 (-)	10,232 bp
Tssr159490	Chr19:44385870-44385877 (-)	10,274 bp
Tssr159489	Chr19:44385768-44385811 (-)	10,358 bp
Tssr159488	Chr19:44385714-44385751 (-)	10,415 bp
Tssr159487	Chr19:44385697-44385708 (-)	10,445 bp
Tssr159486	Chr19:44385616-44385626 (-)	10,527 bp
Tssr159485	Chr19:44385609-44385612 (-)	10,537 bp
Tssr159484	Chr19:44385483-44385494 (-)	10,659 bp
Tssr159483	Chr19:44385449-44385467 (-)	10,690 bp
Tssr159482	Chr19:44385358-44385369 (-)	10,784 bp
Tssr159481	Chr19:44385258-44385281 (-)	10,878 bp
Tssr159480	Chr19:44385209-44385222 (-)	10,932 bp
Tssr159479	Chr19:44385181-44385190 (-)	10,962 bp
Tssr159478	Chr19:44385157-44385172 (-)	10,983 bp
Tssr159477	Chr19:44385147-44385151 (-)	10,999 bp
Tssr159476	Chr19:44385127-44385142 (-)	11,013 bp
Tssr159475	Chr19:44385109-44385124 (-)	11,031 bp
Tssr159474	Chr19:44385064-44385077 (-)	11,077 bp
Tssr159473	Chr19:44385039-44385055 (-)	11,101 bp
Tssr159472	Chr19:44385020-44385036 (-)	11,120 bp
Tssr159471	Chr19:44384984-44385010 (-)	11,151 bp
Tssr159470	Chr19:44384967-44384977 (-)	11,176 bp
Tssr159469	Chr19:44384950-44384963 (-)	11,191 bp
Tssr159468	Chr19:44384880-44384898 (-)	11,259 bp
Tssr5524	Chr19:44384798-44384803 (-)	11,347 bp
Tssr159467	Chr19:44384632-44384652 (-)	11,506 bp
Tssr159466	Chr19:44384579-44384588 (-)	11,564 bp
Tssr159465	Chr19:44384558-44384570 (-)	11,584 bp
Tssr159464	Chr19:44384534-44384550 (-)	11,606 bp
Tssr159463	Chr19:44384511-44384520 (-)	11,632 bp
Tssr159462	Chr19:44384465-44384481 (-)	11,675 bp
Tssr159461	Chr19:44384437-44384449 (-)	11,705 bp
Tssr159460	Chr19:44384378-44384388 (-)	11,765 bp
Tssr159459	Chr19:44384341-44384352 (-)	11,801 bp
Tssr159458	Chr19:44384251-44384260 (-)	11,892 bp
Tssr159457	Chr19:44384221-44384226 (-)	11,924 bp
Tssr159456	Chr19:44384177-44384197 (-)	11,961 bp
Tssr159455	Chr19:44384055-44384078 (-)	12,081 bp
Tssr159454	Chr19:44383762-44383772 (-)	12,381 bp
Tssr159453	Chr19:44383730-44383753 (-)	12,406 bp
Tssr159452	Chr19:44383671-44383684 (-)	12,470 bp
Tssr159451	Chr19:44383381-44383390 (-)	12,762 bp
Tssr159450	Chr19:44383309-44383310 (-)	12,838 bp
Tssr159449	Chr19:44383282-44383296 (-)	12,859 bp
Tssr159448	Chr19:44383230-44383233 (-)	12,916 bp
Tssr159447	Chr19:44383198-44383207 (-)	12,945 bp
Tssr159446	Chr19:44383021-44383032 (-)	13,121 bp

Scd1 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Alcdp2	Chr19, syntenic		J:98587	Microarray analysis was used to identify genes showing alcohol-induced differential expression between inbred strains C57BL/6J and DBA/2J. These genes were then correlated to 6 previously identified alcohol-related QTLs to identify potential candidate genes. Two different Affymetrix microarrays were used in the analysis. Brain expression data from parental strains and 56 (DBA/2J x C57BL/6J)F2 intercross animals were used for analysis. On mouse Chromosome 19, candidate genes for Alcdp2 at 40 cM were identified with modest priority status. These candidate genes are Scd1 (43 cM), Shoc2, Prdx3 (50 cM), and 3 other yet unidentified expressed sequences (ESTs).
Hcs6	Chr19, 38.15 cM		J:80006	In order to elicudate whether or not Scd1 is the gene responsible for hepatocarcinogenesis susceptibility QTL Hcs6, 179 animals from a (BALB/c x C3H/HeJ)F2 cross were typed for markers on mouse Chromosome 19 to observe the segregation of Scd1 and Hcs6. No linkage was observed, therefore the gene responsible for Hcs6 is not Scd1.

*cM position of peak correlated region/marker