HACL1 (2-hydroxyacyl-CoA lyase 1) - Rat Genome Database

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Gene: HACL1 (2-hydroxyacyl-CoA lyase 1) Homo sapiens
Analyze
Symbol: HACL1
Name: 2-hydroxyacyl-CoA lyase 1
RGD ID: 1607054
HGNC Page HGNC:17856
Description: Enables several functions, including 2-hydroxy-3-methylhexadecanoyl-CoA lyase activity; ATP binding activity; and cation binding activity. Involved in fatty acid alpha-oxidation; phytanic acid metabolic process; and protein targeting to peroxisome. Located in nucleoplasm and peroxisome.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1600020H07Rik; 2-HPCL; 2-hydroxyphytanol-CoA lyase; 2-hydroxyphytanoyl-CoA lyase; FLJ55041; HPCL; HPCL2; PHYH2; phytanoyl-CoA 2-hydroxylase 2; phytanoyl-CoA hydroxylase 2
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38315,560,699 - 15,601,569 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl315,560,699 - 15,601,852 (-)EnsemblGRCh38hg38GRCh38
GRCh37315,602,206 - 15,643,076 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36315,577,243 - 15,618,134 (-)NCBINCBI36Build 36hg18NCBI36
Celera315,540,467 - 15,581,279 (-)NCBICelera
Cytogenetic Map3p25.1NCBI
HuRef315,537,616 - 15,578,260 (-)NCBIHuRef
CHM1_1315,553,051 - 15,593,804 (-)NCBICHM1_1
T2T-CHM13v2.0315,563,097 - 15,603,888 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1-naphthyl isothiocyanate  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrabromodibenzodioxine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (ISO)
2,6-dinitrotoluene  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3H-1,2-dithiole-3-thione  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (ISO)
aconitine  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (EXP)
ammonium chloride  (ISO)
Aroclor 1254  (ISO)
arsenous acid  (EXP)
atazanavir sulfate  (EXP)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (ISO)
buspirone  (ISO)
C60 fullerene  (ISO)
carbamazepine  (EXP)
carbon nanotube  (ISO)
carmustine  (ISO)
chenodeoxycholic acid  (EXP)
cholesterol  (ISO)
chromium trinitrate  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP)
clofibrate  (ISO)
clofibric acid  (ISO)
cobalt dichloride  (ISO)
cyclosporin A  (EXP)
decabromodiphenyl ether  (ISO)
deoxycholic acid  (EXP)
diarsenic trioxide  (EXP)
dicrotophos  (EXP)
dioxygen  (ISO)
doxorubicin  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
flutamide  (ISO)
folic acid  (ISO)
furan  (ISO)
glafenine  (ISO)
glycochenodeoxycholic acid  (EXP)
glycocholic acid  (EXP)
glycodeoxycholic acid  (EXP)
ivermectin  (EXP)
methapyrilene  (ISO)
methotrexate  (ISO)
Muraglitazar  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (EXP)
nimesulide  (ISO)
oxycodone  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
perfluorooctanoic acid  (ISO)
pirinixic acid  (EXP,ISO)
potassium chromate  (ISO)
quercetin  (EXP)
resveratrol  (EXP)
sodium arsenite  (EXP)
sunitinib  (EXP)
Tesaglitazar  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (ISO)
tioguanine  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
trovafloxacin  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10468558   PMID:11042152   PMID:12477932   PMID:14561759   PMID:14702039   PMID:15489334   PMID:15644336   PMID:16189514   PMID:16344560   PMID:16756494   PMID:20178365   PMID:21708296  
PMID:21873635   PMID:21900206   PMID:22002062   PMID:22939629   PMID:24323699   PMID:25416956   PMID:26186194   PMID:26344197   PMID:27107014   PMID:28289220   PMID:28514442   PMID:28986522  
PMID:29568061   PMID:30378028   PMID:31586073   PMID:32296183   PMID:33545068   PMID:33729478   PMID:33961781   PMID:34079125  


Genomics

Comparative Map Data
HACL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38315,560,699 - 15,601,569 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl315,560,699 - 15,601,852 (-)EnsemblGRCh38hg38GRCh38
GRCh37315,602,206 - 15,643,076 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36315,577,243 - 15,618,134 (-)NCBINCBI36Build 36hg18NCBI36
Celera315,540,467 - 15,581,279 (-)NCBICelera
Cytogenetic Map3p25.1NCBI
HuRef315,537,616 - 15,578,260 (-)NCBIHuRef
CHM1_1315,553,051 - 15,593,804 (-)NCBICHM1_1
T2T-CHM13v2.0315,563,097 - 15,603,888 (-)NCBIT2T-CHM13v2.0
Hacl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391431,329,183 - 31,364,201 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1431,320,687 - 31,363,243 (-)EnsemblGRCm39 Ensembl
GRCm381431,607,226 - 31,640,965 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1431,598,730 - 31,641,286 (-)EnsemblGRCm38mm10GRCm38
MGSCv371432,420,412 - 32,454,151 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361430,436,235 - 30,469,970 (-)NCBIMGSCv36mm8
Celera1427,864,878 - 27,898,614 (-)NCBICelera
Cytogenetic Map14BNCBI
Hacl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2166,826,881 - 6,863,027 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl166,824,906 - 6,863,027 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx166,830,764 - 6,867,047 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0167,975,662 - 8,011,946 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0166,838,214 - 6,874,501 (-)NCBIRnor_WKY
Rnor_6.0167,720,047 - 7,758,119 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl167,714,465 - 7,758,189 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0167,646,580 - 7,682,704 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4167,073,038 - 7,108,830 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1167,073,036 - 7,108,828 (-)NCBI
Celera168,335,334 - 8,371,457 (+)NCBICelera
Cytogenetic Map16p16NCBI
Hacl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554302,053,640 - 2,096,432 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554302,055,774 - 2,096,260 (-)NCBIChiLan1.0ChiLan1.0
HACL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1315,823,979 - 15,863,982 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl315,823,979 - 15,863,982 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0315,486,897 - 15,526,552 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LOC608697
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12327,069,676 - 27,188,247 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2327,043,917 - 27,162,593 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02327,572,135 - 27,700,471 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12327,271,635 - 27,389,865 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02327,333,444 - 27,451,635 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02327,581,893 - 27,700,406 (+)NCBIUU_Cfam_GSD_1.0
Hacl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118169,684,583 - 169,717,508 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049364732,823,183 - 2,856,077 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HACL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl132,766,514 - 2,840,902 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1132,786,007 - 2,840,882 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2132,714,442 - 2,737,983 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HACL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11560,360,380 - 60,433,528 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1560,322,722 - 60,433,647 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604133,390,238 - 33,465,437 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hacl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248225,079,634 - 5,145,503 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248225,078,925 - 5,189,253 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Position Markers
SHGC-82510  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37315,628,270 - 15,628,556UniSTSGRCh37
Build 36315,603,274 - 15,603,560RGDNCBI36
Celera315,566,498 - 15,566,784RGD
Cytogenetic Map3p25.1UniSTS
HuRef315,563,658 - 15,563,944UniSTS
TNG Radiation Hybrid Map39593.0UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1673
Count of miRNA genes:797
Interacting mature miRNAs:914
Transcripts:ENST00000321169, ENST00000383779, ENST00000414979, ENST00000421993, ENST00000422591, ENST00000435217, ENST00000451445, ENST00000456194, ENST00000457447, ENST00000460907, ENST00000469454, ENST00000472857
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2216 1586 1640 562 1285 419 4166 1559 2117 328 1391 1544 156 1186 2619 4 1
Low 223 1403 86 62 665 46 191 636 1617 91 69 69 19 1 18 169 1 1
Below cutoff 2 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001284413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001284415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001284416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_012260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_104315 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA643224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC027129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF161397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ131753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK056977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK301546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK301990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK302086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC001627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC007440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA609383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB049608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB241165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000321169   ⟹   ENSP00000323811
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,560,699 - 15,601,569 (-)Ensembl
RefSeq Acc Id: ENST00000383779   ⟹   ENSP00000373289
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,560,746 - 15,601,557 (-)Ensembl
RefSeq Acc Id: ENST00000414979   ⟹   ENSP00000395352
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,582,878 - 15,601,561 (-)Ensembl
RefSeq Acc Id: ENST00000421993   ⟹   ENSP00000391393
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,579,900 - 15,601,592 (-)Ensembl
RefSeq Acc Id: ENST00000422591   ⟹   ENSP00000392796
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,563,358 - 15,601,569 (-)Ensembl
RefSeq Acc Id: ENST00000435217   ⟹   ENSP00000395278
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,560,716 - 15,601,569 (-)Ensembl
RefSeq Acc Id: ENST00000451445   ⟹   ENSP00000403656
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,560,746 - 15,601,587 (-)Ensembl
RefSeq Acc Id: ENST00000456194   ⟹   ENSP00000390699
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,560,747 - 15,601,569 (-)Ensembl
RefSeq Acc Id: ENST00000457447   ⟹   ENSP00000404883
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,560,807 - 15,601,569 (-)Ensembl
RefSeq Acc Id: ENST00000460907
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,596,152 - 15,601,569 (-)Ensembl
RefSeq Acc Id: ENST00000469454
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,595,915 - 15,601,185 (-)Ensembl
RefSeq Acc Id: ENST00000472857
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,600,801 - 15,601,546 (-)Ensembl
RefSeq Acc Id: ENST00000628377   ⟹   ENSP00000486684
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl315,560,704 - 15,601,852 (-)Ensembl
RefSeq Acc Id: NM_001284413   ⟹   NP_001271342
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38315,560,699 - 15,601,569 (-)NCBI
HuRef315,537,588 - 15,578,489 (-)NCBI
CHM1_1315,553,023 - 15,594,033 (-)NCBI
T2T-CHM13v2.0315,563,097 - 15,603,888 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001284415   ⟹   NP_001271344
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38315,560,699 - 15,601,569 (-)NCBI
HuRef315,537,588 - 15,578,489 (-)NCBI
CHM1_1315,553,023 - 15,594,033 (-)NCBI
T2T-CHM13v2.0315,563,097 - 15,603,888 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001284416   ⟹   NP_001271345
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38315,560,699 - 15,601,569 (-)NCBI
HuRef315,537,588 - 15,578,489 (-)NCBI
CHM1_1315,553,023 - 15,594,033 (-)NCBI
T2T-CHM13v2.0315,563,097 - 15,603,888 (-)NCBI
Sequence:
RefSeq Acc Id: NM_012260   ⟹   NP_036392
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38315,560,699 - 15,601,569 (-)NCBI
GRCh37315,602,239 - 15,643,359 (-)NCBI
Build 36315,577,243 - 15,618,134 (-)NCBI Archive
Celera315,540,467 - 15,581,279 (-)RGD
HuRef315,537,588 - 15,578,489 (-)NCBI
CHM1_1315,553,023 - 15,594,033 (-)NCBI
T2T-CHM13v2.0315,563,097 - 15,603,888 (-)NCBI
Sequence:
RefSeq Acc Id: NR_104315
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38315,560,699 - 15,601,569 (-)NCBI
HuRef315,537,588 - 15,578,489 (-)NCBI
CHM1_1315,553,023 - 15,594,033 (-)NCBI
T2T-CHM13v2.0315,563,097 - 15,603,888 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036392   ⟸   NM_012260
- Peptide Label: isoform a
- UniProtKB: Q9P0A2 (UniProtKB/Swiss-Prot),   Q9UJ83 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001271342   ⟸   NM_001284413
- Peptide Label: isoform b
- UniProtKB: Q9UJ83 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001271345   ⟸   NM_001284416
- Peptide Label: isoform d
- UniProtKB: Q9UJ83 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001271344   ⟸   NM_001284415
- Peptide Label: isoform c
- UniProtKB: Q9UJ83 (UniProtKB/Swiss-Prot),   B4DXR1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000403656   ⟸   ENST00000451445
RefSeq Acc Id: ENSP00000323811   ⟸   ENST00000321169
RefSeq Acc Id: ENSP00000395352   ⟸   ENST00000414979
RefSeq Acc Id: ENSP00000390699   ⟸   ENST00000456194
RefSeq Acc Id: ENSP00000404883   ⟸   ENST00000457447
RefSeq Acc Id: ENSP00000486684   ⟸   ENST00000628377
RefSeq Acc Id: ENSP00000391393   ⟸   ENST00000421993
RefSeq Acc Id: ENSP00000395278   ⟸   ENST00000435217
RefSeq Acc Id: ENSP00000392796   ⟸   ENST00000422591
RefSeq Acc Id: ENSP00000373289   ⟸   ENST00000383779
Protein Domains
TPP_enzyme_C   TPP_enzyme_M   TPP_enzyme_N

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9UJ83-F1-model_v2 AlphaFold Q9UJ83 1-578 view protein structure

Promoters
RGD ID:6863704
Promoter ID:EPDNEW_H5017
Type:initiation region
Name:HACL1_1
Description:2-hydroxyacyl-CoA lyase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H5019  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38315,601,569 - 15,601,629EPDNEW
RGD ID:6863708
Promoter ID:EPDNEW_H5019
Type:initiation region
Name:HACL1_2
Description:2-hydroxyacyl-CoA lyase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H5017  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38315,601,861 - 15,601,921EPDNEW
RGD ID:6801111
Promoter ID:HG_KWN:43939
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_2Hour,   K562
Transcripts:OTTHUMT00000252104,   OTTHUMT00000342872,   OTTHUMT00000342961,   OTTHUMT00000343008,   OTTHUMT00000343010,   OTTHUMT00000343011,   OTTHUMT00000343265,   OTTHUMT00000343266,   OTTHUMT00000343267,   OTTHUMT00000343268,   UC003CAG.1,   UC010HEP.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36315,617,891 - 15,618,391 (-)MPROMDB
RGD ID:6852010
Promoter ID:EP73811
Type:initiation region
Name:HS_HPCL2
Description:2-hydroxyphytanoyl-CoA lyase.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:NEDO full length human cDNA sequencing project.; Oligo-capping
Position:
Human AssemblyChrPosition (strand)Source
Build 36315,618,080 - 15,618,140EPD

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2
pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:52066-20280127)x3 copy number gain See cases [RCV000051690] Chr3:52066..20280127 [GRCh38]
Chr3:93749..20321619 [GRCh37]
Chr3:68749..20296623 [NCBI36]
Chr3:3p26.3-24.3
pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:52266-29248782)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|See cases [RCV000051718] Chr3:52266..29248782 [GRCh38]
Chr3:93949..29290273 [GRCh37]
Chr3:68949..29265277 [NCBI36]
Chr3:3p26.3-24.1
pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3 copy number gain See cases [RCV000051719] Chr3:63843..19510600 [GRCh38]
Chr3:105526..19552092 [GRCh37]
Chr3:80526..19527096 [NCBI36]
Chr3:3p26.3-24.3
pathogenic
GRCh38/hg38 3p25.3-22.2(chr3:11463328-38919543)x3 copy number gain See cases [RCV000051720] Chr3:11463328..38919543 [GRCh38]
Chr3:11504802..38961034 [GRCh37]
Chr3:11479802..38936038 [NCBI36]
Chr3:3p25.3-22.2
pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1
pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3 copy number gain See cases [RCV000137941] Chr3:32241..20334387 [GRCh38]
Chr3:73914..20375879 [GRCh37]
Chr3:48914..20350883 [NCBI36]
Chr3:3p26.3-24.3
pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1
pathogenic
GRCh38/hg38 3p25.1-24.3(chr3:15304910-16372771)x3 copy number gain See cases [RCV000143403] Chr3:15304910..16372771 [GRCh38]
Chr3:15346417..16414278 [GRCh37]
Chr3:15321421..16389282 [NCBI36]
Chr3:3p25.1-24.3
likely benign
GRCh38/hg38 3p25.1-24.3(chr3:14360747-21656134)x4 copy number gain See cases [RCV000143767] Chr3:14360747..21656134 [GRCh38]
Chr3:14402247..21697626 [GRCh37]
Chr3:14377251..21672630 [NCBI36]
Chr3:3p25.1-24.3
pathogenic
GRCh37/hg19 3p26.3-24.2(chr3:61891-24432821)x3 copy number gain See cases [RCV000447247] Chr3:61891..24432821 [GRCh37]
Chr3:3p26.3-24.2
pathogenic
GRCh37/hg19 3p26.3-22.2(chr3:61891-36710181)x3 copy number gain See cases [RCV000448528] Chr3:61891..36710181 [GRCh37]
Chr3:3p26.3-22.2
pathogenic
GRCh37/hg19 3p26.3-22.3(chr3:61891-33958201)x3 copy number gain See cases [RCV000510429] Chr3:61891..33958201 [GRCh37]
Chr3:3p26.3-22.3
pathogenic
GRCh37/hg19 3p26.3-22.2(chr3:61891-37459464)x3 copy number gain See cases [RCV000511463] Chr3:61891..37459464 [GRCh37]
Chr3:3p26.3-22.2
pathogenic
GRCh37/hg19 3p25.1-24.3(chr3:13720222-17808236)x1 copy number loss See cases [RCV000511037] Chr3:13720222..17808236 [GRCh37]
Chr3:3p25.1-24.3
likely pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-24.3(chr3:1897972-19519085)x3 copy number gain not provided [RCV000682215] Chr3:1897972..19519085 [GRCh37]
Chr3:3p26.3-24.3
pathogenic
GRCh37/hg19 3p26.1-24.3(chr3:5173870-16760262)x3 copy number gain not provided [RCV000682233] Chr3:5173870..16760262 [GRCh37]
Chr3:3p26.1-24.3
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p25.2-24.2(chr3:13276005-24295240)x3 copy number gain not provided [RCV000742260] Chr3:13276005..24295240 [GRCh37]
Chr3:3p25.2-24.2
pathogenic
GRCh37/hg19 3p25.1(chr3:15509327-15607002)x1 copy number loss not provided [RCV000742272] Chr3:15509327..15607002 [GRCh37]
Chr3:3p25.1
uncertain significance
NM_012260.4(HACL1):c.615G>A (p.Thr205=) single nucleotide variant not provided [RCV000946715] Chr3:15582929 [GRCh38]
Chr3:15624436 [GRCh37]
Chr3:3p25.1
benign
NM_012260.4(HACL1):c.952G>A (p.Ala318Thr) single nucleotide variant not provided [RCV000961126] Chr3:15573200 [GRCh38]
Chr3:15614707 [GRCh37]
Chr3:3p25.1
benign
NM_012260.4(HACL1):c.-73T>C single nucleotide variant not provided [RCV001670516] Chr3:15601536 [GRCh38]
Chr3:15643043 [GRCh37]
Chr3:3p25.1
benign
GRCh37/hg19 3p25.1-24.3(chr3:15085863-16402392)x3 copy number gain not provided [RCV001834333] Chr3:15085863..16402392 [GRCh37]
Chr3:3p25.1-24.3
uncertain significance
GRCh37/hg19 3p26.3-24.2(chr3:61891-24432821) copy number gain not specified [RCV002053299] Chr3:61891..24432821 [GRCh37]
Chr3:3p26.3-24.2
pathogenic
GRCh37/hg19 3p26.3-22.2(chr3:61891-36710181) copy number gain not specified [RCV002053300] Chr3:61891..36710181 [GRCh37]
Chr3:3p26.3-22.2
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:17856 AgrOrtholog
COSMIC HACL1 COSMIC
Ensembl Genes ENSG00000131373 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000323811 ENTREZGENE
  ENSP00000323811.5 UniProtKB/Swiss-Prot
  ENSP00000373289.4 UniProtKB/TrEMBL
  ENSP00000390699 ENTREZGENE
  ENSP00000390699.2 UniProtKB/Swiss-Prot
  ENSP00000391393.1 UniProtKB/TrEMBL
  ENSP00000392796.1 UniProtKB/TrEMBL
  ENSP00000395278.2 UniProtKB/TrEMBL
  ENSP00000395352.1 UniProtKB/TrEMBL
  ENSP00000403656 ENTREZGENE
  ENSP00000403656.2 UniProtKB/Swiss-Prot
  ENSP00000404883 ENTREZGENE
  ENSP00000404883.2 UniProtKB/Swiss-Prot
  ENSP00000486684.1 UniProtKB/TrEMBL
Ensembl Transcript ENST00000321169 ENTREZGENE
  ENST00000321169.10 UniProtKB/Swiss-Prot
  ENST00000383779 ENTREZGENE
  ENST00000383779.8 UniProtKB/TrEMBL
  ENST00000414979.1 UniProtKB/TrEMBL
  ENST00000421993.5 UniProtKB/TrEMBL
  ENST00000422591.5 UniProtKB/TrEMBL
  ENST00000435217.6 UniProtKB/TrEMBL
  ENST00000451445 ENTREZGENE
  ENST00000451445.6 UniProtKB/Swiss-Prot
  ENST00000456194 ENTREZGENE
  ENST00000456194.6 UniProtKB/Swiss-Prot
  ENST00000457447 ENTREZGENE
  ENST00000457447.6 UniProtKB/Swiss-Prot
  ENST00000628377.2 UniProtKB/TrEMBL
GTEx ENSG00000131373 GTEx
HGNC ID HGNC:17856 ENTREZGENE
Human Proteome Map HACL1 Human Proteome Map
InterPro DHS-like_NAD/FAD-binding_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HACL1-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  THDP-binding UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thiamin_PyroP_enz_cen_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thiamin_PyroP_enz_TPP-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPP_enzyme-bd_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:26061 UniProtKB/Swiss-Prot
NCBI Gene 26061 ENTREZGENE
OMIM 604300 OMIM
PANTHER PTHR43710 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TPP_enzyme_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPP_enzyme_M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPP_enzyme_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA142671172 PharmGKB
Superfamily-SCOP SSF52467 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52518 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B3KPX4_HUMAN UniProtKB/TrEMBL
  B4DXR1 ENTREZGENE, UniProtKB/TrEMBL
  C9J306_HUMAN UniProtKB/TrEMBL
  C9JJM7_HUMAN UniProtKB/TrEMBL
  F8WCH9_HUMAN UniProtKB/TrEMBL
  HACL1_HUMAN UniProtKB/Swiss-Prot
  Q7Z773_HUMAN UniProtKB/TrEMBL
  Q9P0A2 ENTREZGENE
  Q9UJ83 ENTREZGENE
UniProt Secondary B4DWI1 UniProtKB/Swiss-Prot
  B4DXI5 UniProtKB/Swiss-Prot
  E9PEN4 UniProtKB/Swiss-Prot
  Q9BV42 UniProtKB/Swiss-Prot
  Q9P0A2 UniProtKB/Swiss-Prot