SYCP2 (synaptonemal complex protein 2) - Rat Genome Database

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Gene: SYCP2 (synaptonemal complex protein 2) Homo sapiens
Analyze
Symbol: SYCP2
Name: synaptonemal complex protein 2
RGD ID: 69483
HGNC Page HGNC
Description: Predicted to be involved in animal organ morphogenesis; female meiotic nuclear division; and male meiotic nuclear division. Predicted to localize to condensed chromosome, centromeric region and lateral element. Implicated in spermatogenic failure 1.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: hsSCP2; SCP-2; SCP2; SPGF1; synaptonemal complex lateral element protein
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
GRCh38.p13 Ensembl2059,863,564 - 59,933,655 (-)EnsemblGRCh38hg38GRCh38
GRCh382059,863,277 - 59,933,700 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372058,438,626 - 58,508,692 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362057,872,013 - 57,940,604 (-)NCBINCBI36hg18NCBI36
Build 342057,872,013 - 57,940,604NCBI
Celera2055,179,316 - 55,247,887 (-)NCBI
Cytogenetic Map20q13.33NCBI
HuRef2055,225,354 - 55,294,509 (-)NCBIHuRef
CHM1_12058,339,670 - 58,409,780 (-)NCBICHM1_1
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromosome  (IEA)
lateral element  (IBA,ISS)
nucleus  (IEA,ISO,NAS)
synaptonemal complex  (ISO,NAS)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

Additional References at PubMed
PMID:10341103   PMID:11780052   PMID:12477932   PMID:20378615   PMID:21873635   PMID:26167880   PMID:26334652   PMID:30657449   PMID:31866047  


Genomics

Comparative Map Data
SYCP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2059,863,564 - 59,933,655 (-)EnsemblGRCh38hg38GRCh38
GRCh382059,863,277 - 59,933,700 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372058,438,626 - 58,508,692 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362057,872,013 - 57,940,604 (-)NCBINCBI36hg18NCBI36
Build 342057,872,013 - 57,940,604NCBI
Celera2055,179,316 - 55,247,887 (-)NCBI
Cytogenetic Map20q13.33NCBI
HuRef2055,225,354 - 55,294,509 (-)NCBIHuRef
CHM1_12058,339,670 - 58,409,780 (-)NCBICHM1_1
Sycp2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392177,987,088 - 178,051,580 (-)NCBIGRCm39mm39
GRCm39 Ensembl2177,987,086 - 178,049,478 (-)Ensembl
GRCm382178,345,295 - 178,407,776 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2178,345,293 - 178,407,685 (-)EnsemblGRCm38mm10GRCm38
MGSCv372178,080,000 - 178,142,363 (-)NCBIGRCm37mm9NCBIm37
MGSCv362178,274,701 - 178,333,233 (-)NCBImm8
Celera2182,431,695 - 182,494,066 (-)NCBICelera
Cytogenetic Map2H4NCBI
Sycp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23165,431,715 - 165,502,134 (-)NCBI
Rnor_6.0 Ensembl3173,884,287 - 173,947,018 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03173,884,559 - 173,948,304 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03183,144,181 - 183,206,650 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43167,437,522 - 167,502,083 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13167,343,557 - 167,408,119 (-)NCBI
Celera3167,063,122 - 167,125,089 (+)NCBICelera
Cytogenetic Map3q43NCBI
Sycp2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555283,809,438 - 3,886,312 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555283,809,438 - 3,887,055 (+)NCBIChiLan1.0ChiLan1.0
SYCP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12057,571,625 - 57,639,701 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2057,571,935 - 57,629,016 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02056,219,579 - 56,289,382 (-)NCBIMhudiblu_PPA_v0panPan3
SYCP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12444,471,516 - 44,546,501 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2444,471,828 - 44,546,495 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2443,715,727 - 43,795,976 (-)NCBI
ROS_Cfam_1.02445,337,831 - 45,418,204 (-)NCBI
UMICH_Zoey_3.12444,438,620 - 44,514,644 (-)NCBI
UNSW_CanFamBas_1.02444,557,526 - 44,639,319 (-)NCBI
UU_Cfam_GSD_1.02445,219,139 - 45,299,307 (-)NCBI
Sycp2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640192,810,574 - 192,894,218 (-)NCBI
SpeTri2.0NW_0049365148,264,628 - 8,331,577 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYCP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1759,877,505 - 59,955,209 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11759,875,992 - 59,962,314 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21767,296,749 - 67,373,790 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYCP2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.124,214,713 - 4,283,451 (+)NCBI
ChlSab1.1 Ensembl24,226,063 - 4,282,751 (+)Ensembl
Sycp2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474126,108,446 - 26,208,184 (-)NCBI

Position Markers
RH92762  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372058,438,747 - 58,438,886UniSTSGRCh37
Build 362057,872,142 - 57,872,281RGDNCBI36
Celera2055,179,445 - 55,179,584RGD
Cytogenetic Map20q13.33UniSTS
HuRef2055,225,483 - 55,225,622UniSTS
GeneMap99-GB4 RH Map20339.83UniSTS
SHGC-81285  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372058,439,789 - 58,440,133UniSTSGRCh37
Build 362057,873,184 - 57,873,528RGDNCBI36
Celera2055,180,487 - 55,180,831RGD
Cytogenetic Map20q13.33UniSTS
HuRef2055,226,525 - 55,226,869UniSTS
TNG Radiation Hybrid Map2026787.0UniSTS
SHGC-79529  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372058,467,056 - 58,467,332UniSTSGRCh37
Build 362057,900,451 - 57,900,727RGDNCBI36
Celera2055,207,736 - 55,208,012RGD
Cytogenetic Map20q13.33UniSTS
HuRef2055,253,786 - 55,254,062UniSTS
TNG Radiation Hybrid Map2026787.0UniSTS
SYCP2_9099  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372058,438,944 - 58,439,408UniSTSGRCh37
Build 362057,872,339 - 57,872,803RGDNCBI36
Celera2055,179,642 - 55,180,106RGD
HuRef2055,225,680 - 55,226,144UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:853
Count of miRNA genes:492
Interacting mature miRNAs:532
Transcripts:ENST00000357552, ENST00000371001, ENST00000412613, ENST00000425931, ENST00000446834, ENST00000461538, ENST00000471331, ENST00000474749, ENST00000476314
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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 adipose tissue appendage entire extraembryonic component
High
Medium 20 1 8 4 35 3 65 7 51 16 447 50 2 49
Low 2281 2521 1297 285 1275 132 3621 1604 3512 354 942 1465 160 1202 2242 4
Below cutoff 119 462 409 324 589 321 669 582 153 47 57 87 9 2 497 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_046980 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_014258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011528487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011528488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011528489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011528490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011528493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017027586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017027587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017027588 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017027589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017027590 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017027591 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017027592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AK308889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL080226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL109928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL158092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC040566 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC132864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC132870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC146798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ575787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX648091 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX649108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB443704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB636651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF456972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y08982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000357552   ⟹   ENSP00000350162
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2059,863,571 - 59,933,637 (-)Ensembl
RefSeq Acc Id: ENST00000371001   ⟹   ENSP00000360040
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2059,863,564 - 59,932,154 (-)Ensembl
RefSeq Acc Id: ENST00000412613   ⟹   ENSP00000404358
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2059,864,337 - 59,868,880 (-)Ensembl
RefSeq Acc Id: ENST00000425931   ⟹   ENSP00000399300
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2059,919,537 - 59,933,655 (-)Ensembl
RefSeq Acc Id: ENST00000446834   ⟹   ENSP00000402456
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2059,877,464 - 59,933,361 (-)Ensembl
RefSeq Acc Id: ENST00000461538
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2059,900,777 - 59,912,226 (-)Ensembl
RefSeq Acc Id: ENST00000471331
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2059,911,769 - 59,915,689 (-)Ensembl
RefSeq Acc Id: ENST00000474749
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2059,880,319 - 59,886,811 (-)Ensembl
RefSeq Acc Id: ENST00000476314
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2059,919,317 - 59,921,483 (-)Ensembl
RefSeq Acc Id: NM_014258   ⟹   NP_055073
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,571 - 59,933,637 (-)NCBI
GRCh372058,438,612 - 58,508,704 (-)NCBI
Build 362057,872,013 - 57,940,604 (-)NCBI Archive
Celera2055,179,316 - 55,247,887 (-)RGD
HuRef2055,225,354 - 55,294,509 (-)ENTREZGENE
CHM1_12058,339,670 - 58,409,780 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011528487   ⟹   XP_011526789
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,933,677 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011528488   ⟹   XP_011526790
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,933,292 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011528489   ⟹   XP_011526791
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,933,356 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011528490   ⟹   XP_011526792
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,933,677 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011528493   ⟹   XP_011526795
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,933,700 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017027586   ⟹   XP_016883075
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,932,460 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017027587   ⟹   XP_016883076
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,932,460 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017027588   ⟹   XP_016883077
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,932,461 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017027589   ⟹   XP_016883078
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,932,461 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017027590   ⟹   XP_016883079
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,933,676 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017027591   ⟹   XP_016883080
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,863,277 - 59,915,689 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017027592   ⟹   XP_016883081
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,882,114 - 59,932,463 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_055073   ⟸   NM_014258
- UniProtKB: Q9BX26 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011526789   ⟸   XM_011528487
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_011526792   ⟸   XM_011528490
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_011526795   ⟸   XM_011528493
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_011526791   ⟸   XM_011528489
- Peptide Label: isoform X3
- UniProtKB: Q9BX26 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011526790   ⟸   XM_011528488
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_016883079   ⟸   XM_017027590
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_016883078   ⟸   XM_017027589
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_016883077   ⟸   XM_017027588
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_016883076   ⟸   XM_017027587
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_016883075   ⟸   XM_017027586
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_016883080   ⟸   XM_017027591
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_016883081   ⟸   XM_017027592
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSP00000360040   ⟸   ENST00000371001
RefSeq Acc Id: ENSP00000399300   ⟸   ENST00000425931
RefSeq Acc Id: ENSP00000404358   ⟸   ENST00000412613
RefSeq Acc Id: ENSP00000402456   ⟸   ENST00000446834
RefSeq Acc Id: ENSP00000350162   ⟸   ENST00000357552
Protein Domains
SYCP2_ARLD   SYCP2_SLD

Promoters
RGD ID:6798572
Promoter ID:HG_KWN:40031
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   Jurkat,   K562,   Lymphoblastoid
Transcripts:ENST00000357552,   ENST00000358293,   OTTHUMT00000268132,   OTTHUMT00000268133
Position:
Human AssemblyChrPosition (strand)Source
Build 362057,941,891 - 57,942,607 (+)MPROMDB
RGD ID:13602282
Promoter ID:EPDNEW_H27325
Type:initiation region
Name:SYCP2_3
Description:synaptonemal complex protein 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H27326  EPDNEW_H27327  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,933,358 - 59,933,418EPDNEW
RGD ID:13602284
Promoter ID:EPDNEW_H27326
Type:initiation region
Name:SYCP2_2
Description:synaptonemal complex protein 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H27325  EPDNEW_H27327  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,933,634 - 59,933,694EPDNEW
RGD ID:13602286
Promoter ID:EPDNEW_H27327
Type:initiation region
Name:SYCP2_1
Description:synaptonemal complex protein 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H27325  EPDNEW_H27326  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,933,745 - 59,933,805EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3 copy number gain See cases [RCV000053035] Chr20:44787704..64277321 [GRCh38]
Chr20:43416345..62908674 [GRCh37]
Chr20:42849759..62379118 [NCBI36]
Chr20:20q13.12-13.33		 pathogenic
NM_014258.2(SYCP2):c.1644T>A (p.His548Gln) single nucleotide variant Malignant melanoma [RCV000072733] Chr20:59895458 [GRCh38]
Chr20:58470513 [GRCh37]
Chr20:57903908 [NCBI36]
Chr20:20q13.33		 not provided
NM_014258.4(SYCP2):c.2365-8T>C single nucleotide variant Malignant tumor of prostate [RCV000149208] Chr20:59886842 [GRCh38]
Chr20:58461897 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh38/hg38 20q13.32-13.33(chr20:59041966-64277321)x3 copy number gain See cases [RCV000135805] Chr20:59041966..64277321 [GRCh38]
Chr20:57617021..62908674 [GRCh37]
Chr20:57050416..62379118 [NCBI36]
Chr20:20q13.32-13.33		 pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:55630597-60941207)x3 copy number gain See cases [RCV000135622] Chr20:55630597..60941207 [GRCh38]
Chr20:54220678..59516263 [GRCh37]
Chr20:53639062..58949658 [NCBI36]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:56198032-64277321)x3 copy number gain See cases [RCV000138035] Chr20:56198032..64277321 [GRCh38]
Chr20:54773088..62908674 [GRCh37]
Chr20:54206495..62379118 [NCBI36]
Chr20:20q13.2-13.33		 pathogenic
GRCh38/hg38 20q13.31-13.33(chr20:57229415-64273089)x3 copy number gain See cases [RCV000141347] Chr20:57229415..64273089 [GRCh38]
Chr20:55804471..62904442 [GRCh37]
Chr20:55237878..62374886 [NCBI36]
Chr20:20q13.31-13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:53236165-64284202)x3 copy number gain See cases [RCV000143584] Chr20:53236165..64284202 [GRCh38]
Chr20:51852704..62915555 [GRCh37]
Chr20:51286111..62385999 [NCBI36]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh37/hg19 20q13.33(chr20:58444946-58533817)x3 copy number gain Ductal breast carcinoma [RCV000207310] Chr20:58444946..58533817 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20q13.2-13.33(chr20:51542616-62915555)x3 copy number gain See cases [RCV000511980] Chr20:51542616..62915555 [GRCh37]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555)x3 copy number gain See cases [RCV000510832] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555) copy number gain See cases [RCV000512450] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20q13.32-13.33(chr20:58342058-59978526)x3 copy number gain not provided [RCV000684131] Chr20:58342058..59978526 [GRCh37]
Chr20:20q13.32-13.33		 uncertain significance
GRCh37/hg19 20p13-q13.33(chr20:63244-62948788)x3 copy number gain not provided [RCV000741058] Chr20:63244..62948788 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62961294)x3 copy number gain not provided [RCV000741059] Chr20:63244..62961294 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:58416428-58554011)x3 copy number gain not provided [RCV000741297] Chr20:58416428..58554011 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58436963-58496439)x3 copy number gain not provided [RCV000741298] Chr20:58436963..58496439 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58436963-58500453)x3 copy number gain not provided [RCV000741299] Chr20:58436963..58500453 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58436963-58502456)x3 copy number gain not provided [RCV000741300] Chr20:58436963..58502456 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58436963-58516788)x3 copy number gain not provided [RCV000741301] Chr20:58436963..58516788 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58436963-58524284)x3 copy number gain not provided [RCV000741302] Chr20:58436963..58524284 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58440630-58496439)x3 copy number gain not provided [RCV000741303] Chr20:58440630..58496439 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58440630-58500453)x3 copy number gain not provided [RCV000741304] Chr20:58440630..58500453 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58440630-58502456)x3 copy number gain not provided [RCV000741305] Chr20:58440630..58502456 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58440630-58502648)x3 copy number gain not provided [RCV000741306] Chr20:58440630..58502648 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58440630-58511286)x3 copy number gain not provided [RCV000741307] Chr20:58440630..58511286 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58440630-58516788)x3 copy number gain not provided [RCV000741308] Chr20:58440630..58516788 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58440630-58524284)x3 copy number gain not provided [RCV000741309] Chr20:58440630..58524284 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.33(chr20:58440630-58528449)x3 copy number gain not provided [RCV000741310] Chr20:58440630..58528449 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20p13-q13.33(chr20:63244-62912463)x3 copy number gain not provided [RCV000741057] Chr20:63244..62912463 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
NM_014258.4(SYCP2):c.2016T>C (p.Tyr672=) single nucleotide variant not provided [RCV000948057] Chr20:59892338 [GRCh38]
Chr20:58467393 [GRCh37]
Chr20:20q13.33		 benign
NM_014258.4(SYCP2):c.2885A>G (p.Gln962Arg) single nucleotide variant not provided [RCV000971691] Chr20:59880359 [GRCh38]
Chr20:58455414 [GRCh37]
Chr20:20q13.33		 benign
NM_014258.4(SYCP2):c.2852T>C (p.Ile951Thr) single nucleotide variant not provided [RCV000904072] Chr20:59880392 [GRCh38]
Chr20:58455447 [GRCh37]
Chr20:20q13.33		 benign
NM_014258.4(SYCP2):c.2793_2797del (p.Lys932fs) deletion Cryptozoospermia [RCV000855716]|Oligosynaptic infertility [RCV001005041] Chr20:59880447..59880451 [GRCh38]
Chr20:58455502..58455506 [GRCh37]
Chr20:20q13.33		 pathogenic|likely pathogenic
NM_014258.4(SYCP2):c.2018_2021AGAA[1] (p.Lys674fs) microsatellite Cryptozoospermia [RCV000855717]|Oligosynaptic infertility [RCV001005042] Chr20:59892329..59892332 [GRCh38]
Chr20:58467384..58467387 [GRCh37]
Chr20:20q13.33		 pathogenic|likely pathogenic
GRCh37/hg19 20q13.2-13.33(chr20:54143747-62194881) copy number gain not provided [RCV000767669] Chr20:54143747..62194881 [GRCh37]
Chr20:20q13.2-13.33		 pathogenic
NM_014258.4(SYCP2):c.3023C>T (p.Pro1008Leu) single nucleotide variant not provided [RCV000962817] Chr20:59877512 [GRCh38]
Chr20:58452567 [GRCh37]
Chr20:20q13.33		 benign
NM_014258.4(SYCP2):c.305C>T (p.Ala102Val) single nucleotide variant not provided [RCV000962818] Chr20:59919590 [GRCh38]
Chr20:58494645 [GRCh37]
Chr20:20q13.33		 benign
NM_014258.4(SYCP2):c.3067_3071del (p.Lys1023fs) deletion Early spermatogenesis maturation arrest [RCV000855718]|Oligosynaptic infertility [RCV001005040] Chr20:59877464..59877468 [GRCh38]
Chr20:58452519..58452523 [GRCh37]
Chr20:20q13.33		 pathogenic|likely pathogenic
NM_014258.4(SYCP2):c.2452A>G (p.Ile818Val) single nucleotide variant not provided [RCV000953395] Chr20:59886747 [GRCh38]
Chr20:58461802 [GRCh37]
Chr20:20q13.33		 benign
NM_014258.4(SYCP2):c.4023C>T (p.Asp1341=) single nucleotide variant not provided [RCV000895447] Chr20:59867813 [GRCh38]
Chr20:58442868 [GRCh37]
Chr20:20q13.33		 benign
NM_014258.4(SYCP2):c.4158G>A (p.Thr1386=) single nucleotide variant not provided [RCV000958097] Chr20:59866557 [GRCh38]
Chr20:58441612 [GRCh37]
Chr20:20q13.33		 benign
NM_014258.4(SYCP2):c.95T>C (p.Ile32Thr) single nucleotide variant not provided [RCV000958098] Chr20:59921383 [GRCh38]
Chr20:58496438 [GRCh37]
Chr20:20q13.33		 benign
GRCh37/hg19 20q13.31-13.33(chr20:55743522-62032989)x3 copy number gain not provided [RCV001007097] Chr20:55743522..62032989 [GRCh37]
Chr20:20q13.31-13.33		 pathogenic
GRCh37/hg19 20q13.32-13.33(chr20:56788101-62762405)x3 copy number gain not provided [RCV001007098] Chr20:56788101..62762405 [GRCh37]
Chr20:20q13.32-13.33		 pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:11490 AgrOrtholog
COSMIC SYCP2 COSMIC
Ensembl Genes ENSG00000196074 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000350162 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000360040 UniProtKB/Swiss-Prot
  ENSP00000399300 UniProtKB/TrEMBL
  ENSP00000402456 ENTREZGENE, UniProtKB/TrEMBL
  ENSP00000404358 UniProtKB/TrEMBL
Ensembl Transcript ENST00000357552 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000371001 UniProtKB/Swiss-Prot
  ENST00000412613 UniProtKB/TrEMBL
  ENST00000425931 UniProtKB/TrEMBL
  ENST00000446834 ENTREZGENE, UniProtKB/TrEMBL
GTEx ENSG00000196074 GTEx
HGNC ID HGNC:11490 ENTREZGENE
Human Proteome Map SYCP2 Human Proteome Map
InterPro SYCP1/2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYCP2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYCP2_ARLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYCP2_SLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:10388 UniProtKB/Swiss-Prot
NCBI Gene 10388 ENTREZGENE
OMIM 258150 OMIM
  604105 OMIM
PANTHER PTHR15607 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR15607:SF12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SYCP2_ARLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYCP2_SLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA36272 PharmGKB
UniProt A2A2M9_HUMAN UniProtKB/TrEMBL
  A2A340_HUMAN UniProtKB/TrEMBL
  A2A341_HUMAN UniProtKB/TrEMBL
  A6QL60_HUMAN UniProtKB/TrEMBL
  Q8IWA1_HUMAN UniProtKB/TrEMBL
  Q9BX26 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A2RUE5 UniProtKB/Swiss-Prot
  O75763 UniProtKB/Swiss-Prot
  Q5JX11 UniProtKB/Swiss-Prot
  Q9NTX8 UniProtKB/Swiss-Prot
  Q9UG27 UniProtKB/Swiss-Prot