PRIM1 (DNA primase subunit 1) - Rat Genome Database

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Gene: PRIM1 (DNA primase subunit 1) Homo sapiens
Analyze
Symbol: PRIM1
Name: DNA primase subunit 1
RGD ID: 1348091
HGNC Page HGNC:9369
Description: Enables DNA primase activity; metal ion binding activity; and ribonucleotide binding activity. Involved in DNA replication initiation and DNA replication, synthesis of RNA primer. Located in membrane. Part of alpha DNA polymerase:primase complex.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: DNA primase 1; DNA primase 49 kDa subunit; DNA primase small subunit; DNA primase subunit 48; MGC12308; p49; PDIL; primase (DNA) subunit 1; primase p49 subunit; primase polypeptide 1, 49kDa; primase, DNA, polypeptide 1 (49kDa); primase, polypeptide 1, 49kda
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: AL512637.1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381256,731,580 - 56,752,323 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1256,730,438 - 56,752,374 (-)EnsemblGRCh38hg38GRCh38
GRCh371257,125,364 - 57,146,107 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361255,411,631 - 55,432,413 (-)NCBINCBI36Build 36hg18NCBI36
Build 341255,411,632 - 55,432,413NCBI
Celera1256,779,329 - 56,800,102 (-)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1254,164,017 - 54,185,223 (-)NCBIHuRef
CHM1_11257,092,951 - 57,113,728 (-)NCBICHM1_1
T2T-CHM13v2.01256,699,510 - 56,720,267 (-)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
(-)-demecolcine  (EXP)
(-)-epigallocatechin 3-gallate  (EXP)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (ISO)
2-palmitoylglycerol  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3H-1,2-dithiole-3-thione  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (EXP)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
acetamide  (ISO)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP)
azathioprine  (EXP)
benzo[a]pyrene  (EXP)
benzo[a]pyrene diol epoxide I  (EXP)
benzo[b]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
cadmium dichloride  (ISO)
calcitriol  (EXP)
cannabidiol  (EXP)
carbon nanotube  (ISO)
cefaloridine  (ISO)
chlorpyrifos  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (EXP)
cobalt dichloride  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (EXP)
corticosterone  (ISO)
coumestrol  (EXP)
cyclosporin A  (EXP)
dibutyl phthalate  (ISO)
dicrotophos  (EXP)
dioxygen  (EXP)
diquat  (ISO)
Enterolactone  (EXP)
ethanol  (ISO)
flutamide  (ISO)
folic acid  (EXP,ISO)
genistein  (EXP)
kojic acid  (EXP)
leflunomide  (ISO)
lipopolysaccharide  (EXP)
lucanthone  (EXP)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
methotrexate  (EXP)
methyl methanesulfonate  (EXP)
methylmercury chloride  (EXP)
N-(6-acetamidohexyl)acetamide  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (EXP)
oxaliplatin  (ISO)
ozone  (EXP,ISO)
palbociclib  (EXP)
paracetamol  (EXP,ISO)
PCB138  (ISO)
pentachlorophenol  (ISO)
perfluorohexanesulfonic acid  (ISO)
phenethyl isothiocyanate  (EXP)
phenformin  (ISO)
phenobarbital  (ISO)
phytoestrogen  (EXP)
pirinixic acid  (ISO)
potassium chromate  (EXP)
resveratrol  (EXP)
rotenone  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (EXP)
silicon dioxide  (EXP,ISO)
simvastatin  (EXP)
sodium arsenite  (EXP)
sunitinib  (EXP)
temozolomide  (EXP)
testosterone  (EXP)
tetrachloromethane  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (EXP)
trovafloxacin  (ISO)
tunicamycin  (EXP)
urethane  (EXP)
valproic acid  (EXP)
vincristine  (EXP)
vorinostat  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
11 pairs of ribs  (IAGP)
Absence of subcutaneous fat  (IAGP)
Accessory spleen  (IAGP)
Acute respiratory distress syndrome  (IAGP)
Anemia  (IAGP)
Atrial septal defect  (IAGP)
Autosomal recessive inheritance  (IAGP)
Blepharophimosis  (IAGP)
Broad forehead  (IAGP)
Cataract  (IAGP)
Chronic lung disease  (IAGP)
Cough  (IAGP)
Craniosynostosis  (IAGP)
Cryptorchidism  (IAGP)
Decreased circulating IgA level  (IAGP)
Decreased circulating IgG level  (IAGP)
Decreased circulating total IgM  (IAGP)
Delayed cranial suture closure  (IAGP)
Delayed gross motor development  (IAGP)
Depressed nasal bridge  (IAGP)
Depressed nasal tip  (IAGP)
Elevated circulating alkaline phosphatase concentration  (IAGP)
Elevated circulating hepatic transaminase concentration  (IAGP)
Exocrine pancreatic insufficiency  (IAGP)
Feeding difficulties  (IAGP)
Fetal onset  (IAGP)
Frontal bossing  (IAGP)
Hepatic fibrosis  (IAGP)
Hip dysplasia  (IAGP)
Hypothyroidism  (IAGP)
Intrauterine growth retardation  (IAGP)
Low-set ears  (IAGP)
Lymphopenia  (IAGP)
Macronodular cirrhosis  (IAGP)
Microcephaly  (IAGP)
Microdontia  (IAGP)
Micrognathia  (IAGP)
Microphthalmia  (IAGP)
Microtia  (IAGP)
Patent ductus arteriosus  (IAGP)
Patent foramen ovale  (IAGP)
Portal hypertension  (IAGP)
Premature ovarian insufficiency  (IAGP)
Pulmonary arterial hypertension  (IAGP)
Pulmonary infiltrates  (IAGP)
Recurrent infections  (IAGP)
Renal hypoplasia  (IAGP)
Respiratory insufficiency  (IAGP)
Scaphocephaly  (IAGP)
Severe B lymphocytopenia  (IAGP)
Severe global developmental delay  (IAGP)
Severe postnatal growth retardation  (IAGP)
Small hand  (IAGP)
Smooth philtrum  (IAGP)
Sparse hair  (IAGP)
Tapered finger  (IAGP)
Thick vermilion border  (IAGP)
Thrombocytopenia  (IAGP)
Wheezing  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:6693436   PMID:8026492   PMID:8125298   PMID:8530050   PMID:9268648   PMID:9705292   PMID:9822671   PMID:10441007   PMID:10504261   PMID:11473323   PMID:11917009   PMID:12393188  
PMID:12477932   PMID:15489334   PMID:16169070   PMID:17035231   PMID:19615732   PMID:19946888   PMID:20030400   PMID:21145461   PMID:21873635   PMID:22267201   PMID:22593576   PMID:22658674  
PMID:22678362   PMID:22939629   PMID:22990118   PMID:23891004   PMID:24043831   PMID:24797263   PMID:25550159   PMID:26186194   PMID:26344197   PMID:26496610   PMID:26710848   PMID:26972000  
PMID:26975377   PMID:27599756   PMID:27880917   PMID:28514442   PMID:28718761   PMID:28757209   PMID:29229926   PMID:29568061   PMID:30097999   PMID:30257222   PMID:30446220   PMID:30561431  
PMID:30890647   PMID:30948266   PMID:31091453   PMID:32296183   PMID:32353859   PMID:32416067   PMID:32576198   PMID:32632277   PMID:32814053   PMID:32908930   PMID:32994395   PMID:33060197  
PMID:33961781   PMID:34373451   PMID:34376693   PMID:34719824   PMID:35256949   PMID:35439318   PMID:35509820   PMID:35831314   PMID:36215168   PMID:36526897   PMID:37827155  


Genomics

Comparative Map Data
PRIM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381256,731,580 - 56,752,323 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1256,730,438 - 56,752,374 (-)EnsemblGRCh38hg38GRCh38
GRCh371257,125,364 - 57,146,107 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361255,411,631 - 55,432,413 (-)NCBINCBI36Build 36hg18NCBI36
Build 341255,411,632 - 55,432,413NCBI
Celera1256,779,329 - 56,800,102 (-)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1254,164,017 - 54,185,223 (-)NCBIHuRef
CHM1_11257,092,951 - 57,113,728 (-)NCBICHM1_1
T2T-CHM13v2.01256,699,510 - 56,720,267 (-)NCBIT2T-CHM13v2.0
Prim1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910127,851,084 - 127,865,899 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10127,851,041 - 127,865,906 (+)EnsemblGRCm39 Ensembl
GRCm3810128,015,215 - 128,030,030 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,015,168 - 128,030,037 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710127,452,271 - 127,467,086 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610127,418,164 - 127,432,979 (+)NCBIMGSCv36mm8
Celera10130,410,422 - 130,425,144 (+)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1076.39NCBI
Prim1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr871,031,436 - 1,047,134 (+)NCBIGRCr8
mRatBN7.27446,342 - 462,526 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7431,805 - 462,526 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx73,205,126 - 3,220,740 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.075,081,138 - 5,096,753 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.075,379,312 - 5,394,371 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.072,435,524 - 2,451,169 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,435,553 - 2,451,165 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,415,106 - 2,430,940 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,293,137 - 1,323,029 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.171,293,147 - 1,321,776 (+)NCBI
Celera7325,353 - 341,972 (+)NCBICelera
Cytogenetic Map7q11NCBI
Prim1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554584,275,517 - 4,294,257 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554584,265,500 - 4,294,329 (-)NCBIChiLan1.0ChiLan1.0
PRIM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21037,570,526 - 37,594,933 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11237,567,295 - 37,591,702 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01232,155,541 - 32,176,363 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11232,408,929 - 32,428,734 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1232,408,929 - 32,428,734 (+)Ensemblpanpan1.1panPan2
PRIM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110951,888 - 975,966 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha101,016,706 - 1,040,803 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.010963,062 - 987,154 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl10963,379 - 987,127 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.110940,115 - 964,262 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0101,182,031 - 1,206,116 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0101,306,679 - 1,330,830 (-)NCBIUU_Cfam_GSD_1.0
Prim1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494557,815,995 - 57,836,332 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366461,036,777 - 1,054,108 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366461,033,921 - 1,054,203 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRIM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl522,062,989 - 22,089,436 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1522,064,248 - 22,089,441 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2523,800,887 - 23,824,231 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRIM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11152,676,890 - 52,699,337 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1152,674,602 - 52,699,294 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037193,277,385 - 193,299,812 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prim1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480211,289,391 - 11,316,958 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480211,288,654 - 11,312,401 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in PRIM1
21 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_000946.2(PRIM1):c.1258T>A (p.Phe420Ile) single nucleotide variant Malignant melanoma [RCV000070118] Chr12:56731720 [GRCh38]
Chr12:57125504 [GRCh37]
Chr12:55411771 [NCBI36]
Chr12:12q13.3
not provided
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3 copy number gain See cases [RCV000258805] Chr12:1..133851895 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic|likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902) copy number gain See cases [RCV000511643] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
NM_000946.3(PRIM1):c.592G>A (p.Val198Ile) single nucleotide variant Inborn genetic diseases [RCV003248360] Chr12:56744111 [GRCh38]
Chr12:57137895 [GRCh37]
Chr12:12q13.3
uncertain significance
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
NM_000946.3(PRIM1):c.1255G>T (p.Asp419Tyr) single nucleotide variant Inborn genetic diseases [RCV003273594] Chr12:56731723 [GRCh38]
Chr12:57125507 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.14A>C (p.Asp5Ala) single nucleotide variant not provided [RCV001647852] Chr12:56752285 [GRCh38]
Chr12:57146069 [GRCh37]
Chr12:12q13.3
benign
GRCh37/hg19 12q13.2-14.1(chr12:55552371-62126304)x3 copy number gain not provided [RCV001006505] Chr12:55552371..62126304 [GRCh37]
Chr12:12q13.2-14.1
pathogenic
NM_000946.3(PRIM1):c.901T>C (p.Cys301Arg) single nucleotide variant Microcephalic primordial dwarfism [RCV001261403]|Primordial dwarfism-immunodeficiency-lipodystrophy syndrome [RCV002274169] Chr12:56741516 [GRCh38]
Chr12:57135300 [GRCh37]
Chr12:12q13.3
pathogenic
NM_000946.3(PRIM1):c.103+1G>T single nucleotide variant Microcephalic primordial dwarfism [RCV001261402]|Primordial dwarfism-immunodeficiency-lipodystrophy syndrome [RCV002274168] Chr12:56752195 [GRCh38]
Chr12:57145979 [GRCh37]
Chr12:12q13.3
pathogenic
NM_000946.3(PRIM1):c.638+36C>G single nucleotide variant Microcephalic primordial dwarfism [RCV001261401]|Primordial dwarfism-immunodeficiency-lipodystrophy syndrome [RCV002274167] Chr12:56744029 [GRCh38]
Chr12:57137813 [GRCh37]
Chr12:12q13.3
pathogenic
NM_000946.3(PRIM1):c.873G>T (p.Trp291Cys) single nucleotide variant Premature ovarian failure [RCV001270222] Chr12:56741544 [GRCh38]
Chr12:57135328 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.103+2T>G single nucleotide variant not provided [RCV002275985] Chr12:56752194 [GRCh38]
Chr12:57145978 [GRCh37]
Chr12:12q13.3
likely pathogenic
Single allele duplication not specified [RCV002286382] Chr12:55986511..56885590 [GRCh38]
Chr12:12q13.2-13.3
uncertain significance
NM_000946.3(PRIM1):c.455T>G (p.Phe152Cys) single nucleotide variant Inborn genetic diseases [RCV002688962] Chr12:56746169 [GRCh38]
Chr12:57139953 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.802C>T (p.Arg268Cys) single nucleotide variant Inborn genetic diseases [RCV002818953] Chr12:56741784 [GRCh38]
Chr12:57135568 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.1217G>A (p.Arg406Gln) single nucleotide variant Inborn genetic diseases [RCV002689657] Chr12:56734173 [GRCh38]
Chr12:57127957 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.493G>A (p.Val165Ile) single nucleotide variant Inborn genetic diseases [RCV002693476] Chr12:56746131 [GRCh38]
Chr12:57139915 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.80A>G (p.Tyr27Cys) single nucleotide variant Inborn genetic diseases [RCV003190173] Chr12:56752219 [GRCh38]
Chr12:57146003 [GRCh37]
Chr12:12q13.3
uncertain significance
GRCh37/hg19 12q13.3-14.1(chr12:57064059-59314016)x1 copy number loss not provided [RCV003222783] Chr12:57064059..59314016 [GRCh37]
Chr12:12q13.3-14.1
likely pathogenic
NM_000946.3(PRIM1):c.349G>A (p.Asp117Asn) single nucleotide variant Inborn genetic diseases [RCV003174287] Chr12:56746945 [GRCh38]
Chr12:57140729 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.1063C>T (p.Arg355Cys) single nucleotide variant Inborn genetic diseases [RCV003285609] Chr12:56738515 [GRCh38]
Chr12:57132299 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.629C>T (p.Pro210Leu) single nucleotide variant Inborn genetic diseases [RCV003381359] Chr12:56744074 [GRCh38]
Chr12:57137858 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.98G>A (p.Gly33Asp) single nucleotide variant Inborn genetic diseases [RCV003376993] Chr12:56752201 [GRCh38]
Chr12:57145985 [GRCh37]
Chr12:12q13.3
uncertain significance
NM_000946.3(PRIM1):c.1126G>A (p.Val376Ile) single nucleotide variant not provided [RCV003456814] Chr12:56738452 [GRCh38]
Chr12:57132236 [GRCh37]
Chr12:12q13.3
likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:816
Count of miRNA genes:600
Interacting mature miRNAs:671
Transcripts:ENST00000338193, ENST00000546761, ENST00000548173, ENST00000549549, ENST00000550224, ENST00000550770, ENST00000552408, ENST00000552590
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.

Markers in Region
RH70897  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371247,207,045 - 247,207,245UniSTSGRCh37
Build 361245,273,668 - 245,273,868RGDNCBI36
Celera1220,503,282 - 220,503,482RGD
Cytogenetic Map12q13UniSTS
Cytogenetic Map1q44UniSTS
HuRef1217,601,286 - 217,601,486UniSTS
GeneMap99-GB4 RH Map1766.33UniSTS
NCBI RH Map12001.5UniSTS


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 225 18 87 71 801 75 361 58 352 91 647 297 9 2 45 3
Low 2213 2847 1614 539 1126 376 3990 2049 3307 317 812 1315 166 1 1201 2737 3 2
Below cutoff 1 126 25 14 24 14 6 90 75 11 1 1 1 6

Sequence


RefSeq Acc Id: ENST00000338193   ⟹   ENSP00000350491
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,731,580 - 56,752,323 (-)Ensembl
RefSeq Acc Id: ENST00000546761
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,746,033 - 56,752,269 (-)Ensembl
RefSeq Acc Id: ENST00000548173
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,746,146 - 56,752,339 (-)Ensembl
RefSeq Acc Id: ENST00000549549   ⟹   ENSP00000449806
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,738,465 - 56,743,098 (-)Ensembl
RefSeq Acc Id: ENST00000550224
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,743,514 - 56,752,313 (-)Ensembl
RefSeq Acc Id: ENST00000550770   ⟹   ENSP00000450185
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,741,443 - 56,752,323 (-)Ensembl
RefSeq Acc Id: ENST00000552408
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,746,956 - 56,751,815 (-)Ensembl
RefSeq Acc Id: ENST00000552590   ⟹   ENSP00000448178
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,731,596 - 56,752,373 (-)Ensembl
RefSeq Acc Id: ENST00000672280   ⟹   ENSP00000500157
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,731,296 - 56,752,374 (-)Ensembl
RefSeq Acc Id: ENST00000706566   ⟹   ENSP00000516451
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,730,438 - 56,752,374 (-)Ensembl
RefSeq Acc Id: ENST00000706567   ⟹   ENSP00000516452
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1256,733,782 - 56,752,374 (-)Ensembl
RefSeq Acc Id: NM_000946   ⟹   NP_000937
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381256,731,580 - 56,752,323 (-)NCBI
GRCh371257,125,364 - 57,146,146 (-)ENTREZGENE
Build 361255,411,631 - 55,432,413 (-)NCBI Archive
HuRef1254,164,017 - 54,185,223 (-)ENTREZGENE
CHM1_11257,092,951 - 57,113,728 (-)NCBI
T2T-CHM13v2.01256,699,510 - 56,720,267 (-)NCBI
Sequence:
RefSeq Acc Id: NP_000937   ⟸   NM_000946
- UniProtKB: P49642 (UniProtKB/Swiss-Prot),   B2RBY4 (UniProtKB/TrEMBL),   Q53F98 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000350491   ⟸   ENST00000338193
RefSeq Acc Id: ENSP00000449806   ⟸   ENST00000549549
RefSeq Acc Id: ENSP00000450185   ⟸   ENST00000550770
RefSeq Acc Id: ENSP00000448178   ⟸   ENST00000552590
RefSeq Acc Id: ENSP00000500157   ⟸   ENST00000672280
RefSeq Acc Id: ENSP00000516452   ⟸   ENST00000706567
RefSeq Acc Id: ENSP00000516451   ⟸   ENST00000706566

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P49642-F1-model_v2 AlphaFold P49642 1-420 view protein structure

Promoters
RGD ID:6790380
Promoter ID:HG_KWN:15928
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000338193,   NM_000946,   UC001SME.1,   UC001SMF.1,   UC009ZOZ.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361255,431,956 - 55,432,456 (-)MPROMDB
RGD ID:6853490
Promoter ID:EP74571
Type:initiation region
Name:HS_PRIM1
Description:Primase, polypeptide 1, 49kDa.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Mammalian gene collection (MGC) full-length cDNA cloning
Position:
Human AssemblyChrPosition (strand)Source
Build 361255,432,374 - 55,432,434EPD
RGD ID:7224463
Promoter ID:EPDNEW_H17978
Type:initiation region
Name:PRIM1_1
Description:primase subunit 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381256,752,323 - 56,752,383EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:9369 AgrOrtholog
COSMIC PRIM1 COSMIC
Ensembl Genes ENSG00000198056 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000338193 ENTREZGENE
  ENST00000338193.11 UniProtKB/Swiss-Prot
  ENST00000549549.1 UniProtKB/TrEMBL
  ENST00000550770.1 UniProtKB/TrEMBL
  ENST00000552590.6 UniProtKB/TrEMBL
  ENST00000672280.1 UniProtKB/TrEMBL
  ENST00000706566.1 UniProtKB/Swiss-Prot
  ENST00000706567.1 UniProtKB/TrEMBL
Gene3D-CATH DNA primase, PRIM domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000198056 GTEx
HGNC ID HGNC:9369 ENTREZGENE
Human Proteome Map PRIM1 Human Proteome Map
InterPro DNA_primase_S UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_primase_ssu_euk/arc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:5557 UniProtKB/Swiss-Prot
NCBI Gene 5557 ENTREZGENE
OMIM 176635 OMIM
PANTHER DNA PRIMASE SMALL SUBUNIT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10536 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DNA_primase_S UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA33739 PharmGKB
Superfamily-SCOP Prim-pol domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A5F9ZHB6_HUMAN UniProtKB/TrEMBL
  A0A9L9PXM3_HUMAN UniProtKB/TrEMBL
  B2RBY4 ENTREZGENE, UniProtKB/TrEMBL
  F8VNY2_HUMAN UniProtKB/TrEMBL
  F8VSB2_HUMAN UniProtKB/TrEMBL
  H0YIP2_HUMAN UniProtKB/TrEMBL
  P49642 ENTREZGENE, UniProtKB/Swiss-Prot
  Q53F98 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-08-15 PRIM1  DNA primase subunit 1  PRIM1  primase (DNA) subunit 1  Symbol and/or name change 5135510 APPROVED
2016-03-14 PRIM1  primase (DNA) subunit 1  PRIM1  primase, DNA, polypeptide 1 (49kDa)  Symbol and/or name change 5135510 APPROVED