SMCP (sperm mitochondria associated cysteine rich protein) - Rat Genome Database

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Gene: SMCP (sperm mitochondria associated cysteine rich protein) Homo sapiens
Analyze
Symbol: SMCP
Name: sperm mitochondria associated cysteine rich protein
RGD ID: 737432
HGNC Page HGNC:6962
Description: Predicted to be involved in flagellated sperm motility and penetration of zona pellucida. Predicted to act upstream of or within binding activity of sperm to zona pellucida. Predicted to be located in mitochondrion.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: HSMCSGEN1; MCS; MCSP; MGC26305; MGC26519; mitochondrial capsule selenoprotein; sperm mitochondrial-associated cysteine-rich protein; testicular tissue protein Li 119; testicular tissue protein Li 161
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Pig
Green Monkey
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
GRCh381152,878,322 - 152,885,047 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,878,322 - 152,885,047 (+)EnsemblGRCh38hg38GRCh38
GRCh371152,850,798 - 152,857,523 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,117,422 - 151,124,147 (+)NCBINCBI36Build 36hg18NCBI36
Build 341149,663,870 - 149,670,594NCBI
Celera1125,921,062 - 125,927,787 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,213,780 - 124,220,627 (+)NCBIHuRef
CHM1_11154,246,164 - 154,252,889 (+)NCBICHM1_1
T2T-CHM13v2.01152,014,877 - 152,021,694 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IEA,ISS)
membrane  (IEA)
mitochondrial membrane  (IEA)
mitochondrion  (IEA,ISS)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1418626   PMID:2715306   PMID:8833144   PMID:8916043   PMID:10411523   PMID:11375445   PMID:11940662   PMID:12477932   PMID:15489334   PMID:16189514   PMID:16325371   PMID:17047026  
PMID:18029348   PMID:24244262   PMID:25416956   PMID:31515488   PMID:32296183   PMID:36949045  


Genomics

Comparative Map Data
SMCP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381152,878,322 - 152,885,047 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1152,878,322 - 152,885,047 (+)EnsemblGRCh38hg38GRCh38
GRCh371152,850,798 - 152,857,523 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361151,117,422 - 151,124,147 (+)NCBINCBI36Build 36hg18NCBI36
Build 341149,663,870 - 149,670,594NCBI
Celera1125,921,062 - 125,927,787 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1124,213,780 - 124,220,627 (+)NCBIHuRef
CHM1_11154,246,164 - 154,252,889 (+)NCBICHM1_1
T2T-CHM13v2.01152,014,877 - 152,021,694 (+)NCBIT2T-CHM13v2.0
Smcp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39392,491,173 - 92,496,380 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl392,491,174 - 92,496,304 (-)EnsemblGRCm39 Ensembl
GRCm38392,583,866 - 92,589,073 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl392,583,867 - 92,588,997 (-)EnsemblGRCm38mm10GRCm38
MGSCv37392,387,788 - 92,392,946 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36392,669,263 - 92,674,397 (-)NCBIMGSCv36mm8
Celera394,494,091 - 94,499,188 (+)NCBICelera
Cytogenetic Map3F1NCBI
cM Map340.14NCBI
Smcp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82180,856,561 - 180,861,564 (-)NCBIGRCr8
mRatBN7.22178,160,948 - 178,165,951 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2178,160,127 - 178,166,001 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2185,715,981 - 185,721,012 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02183,696,589 - 183,701,639 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02178,359,078 - 178,364,109 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02192,775,425 - 192,780,631 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2192,775,437 - 192,780,631 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02212,089,678 - 212,094,884 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42185,570,158 - 185,575,161 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12185,520,265 - 185,525,267 (-)NCBI
Celera2172,092,501 - 172,097,504 (+)NCBICelera
RH 3.4 Map21175.1RGD
Cytogenetic Map2q34NCBI
SMCP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2196,958,803 - 96,966,126 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1196,709,982 - 96,717,308 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01128,222,932 - 128,229,417 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11131,853,465 - 131,859,862 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1131,859,238 - 131,859,588 (+)Ensemblpanpan1.1panPan2
SMCP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11761,694,605 - 61,699,122 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1761,694,605 - 61,699,225 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1761,162,443 - 61,166,960 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01762,839,414 - 62,844,100 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1762,839,076 - 62,844,223 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11761,570,495 - 61,574,965 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01761,640,001 - 61,644,684 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01762,397,596 - 62,402,134 (+)NCBIUU_Cfam_GSD_1.0
SMCP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl496,671,907 - 96,676,426 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1496,671,907 - 96,676,426 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24105,607,727 - 105,612,246 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMCP
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12010,838,176 - 10,844,211 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2010,838,452 - 10,838,799 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603810,308,432 - 10,315,187 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in SMCP
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh37/hg19 1q21.1-21.3(chr1:144927578-153223600)x3 copy number gain Chromosome 1q21.1 duplication syndrome [RCV000223957] Chr1:144927578..153223600 [GRCh37]
Chr1:1q21.1-21.3		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1q21.3(chr1:150853044-154647786)x3 copy number gain not provided [RCV000684655] Chr1:150853044..154647786 [GRCh37]
Chr1:1q21.3		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
NC_000001.10:g.(?_149895434)_(156851434_?)dup duplication Autosomal recessive mendelian susceptibility to mycobacterial diseases due to complete RORgamma receptor deficiency [RCV001958273]|Congenital neutropenia-myelofibrosis-nephromegaly syndrome [RCV001958271]|Kostmann syndrome [RCV003120769]|MHC class II deficiency [RCV001992607] Chr1:149895434..156851434 [GRCh37]
Chr1:1q21.2-23.1		 uncertain significance
GRCh37/hg19 1q21.3(chr1:152648864-153286218)x3 copy number gain not provided [RCV002475654] Chr1:152648864..153286218 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_030663.3(SMCP):c.157C>T (p.Pro53Ser) single nucleotide variant Inborn genetic diseases [RCV002773979] Chr1:152884579 [GRCh38]
Chr1:152857055 [GRCh37]
Chr1:1q21.3		 uncertain significance
NM_030663.3(SMCP):c.210G>T (p.Arg70Ser) single nucleotide variant Inborn genetic diseases [RCV002757121] Chr1:152884632 [GRCh38]
Chr1:152857108 [GRCh37]
Chr1:1q21.3		 uncertain significance
GRCh37/hg19 1q12-23.1(chr1:142535935-157648813)x3 copy number gain Chromosome 1q21.1 duplication syndrome [RCV003329522] Chr1:142535935..157648813 [GRCh37]
Chr1:1q12-23.1		 pathogenic
GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3 copy number gain not specified [RCV003986717] Chr1:144368497..158992086 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
GRCh37/hg19 1q21.1-23.1(chr1:146577511-157155587)x3 copy number gain not specified [RCV003987261] Chr1:146577511..157155587 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:250
Count of miRNA genes:190
Interacting mature miRNAs:194
Transcripts:ENST00000368765
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.

Markers in Region
SGC35666  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371152,857,263 - 152,857,464UniSTSGRCh37
Build 361151,123,887 - 151,124,088RGDNCBI36
Celera1125,927,527 - 125,927,728RGD
Cytogenetic Map1q21.3UniSTS
HuRef1124,220,367 - 124,220,568UniSTS
G34873  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371152,857,310 - 152,857,459UniSTSGRCh37
Build 361151,123,934 - 151,124,083RGDNCBI36
Celera1125,927,574 - 125,927,723RGD
Cytogenetic Map1q21.3UniSTS
HuRef1124,220,414 - 124,220,563UniSTS


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
High 289
Medium 3 6 1 2 1 9 3 3 87 7 1 5
Low 104 86 96 22 29 12 177 44 527 11 123 81 10 58 100
Below cutoff 1009 911 649 221 526 135 1510 762 1232 68 399 496 86 356 937

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000368765   ⟹   ENSP00000357754
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1152,878,322 - 152,885,047 (+)Ensembl
RefSeq Acc Id: NM_030663   ⟹   NP_109588
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,878,322 - 152,885,047 (+)NCBI
GRCh371152,850,798 - 152,857,523 (+)RGD
Build 361151,117,422 - 151,124,147 (+)NCBI Archive
Celera1125,921,062 - 125,927,787 (+)RGD
HuRef1124,213,780 - 124,220,627 (+)RGD
CHM1_11154,246,164 - 154,252,889 (+)NCBI
T2T-CHM13v2.01152,014,877 - 152,021,694 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_109588   ⟸   NM_030663
- UniProtKB: Q96A42 (UniProtKB/Swiss-Prot),   P49901 (UniProtKB/Swiss-Prot),   Q5T7P5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000357754   ⟸   ENST00000368765

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P49901-F1-model_v2 AlphaFold P49901 1-116 view protein structure

Promoters
RGD ID:6857150
Promoter ID:EPDNEW_H1740
Type:initiation region
Name:SMCP_2
Description:sperm mitochondria associated cysteine rich protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H1741  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,870,060 - 152,870,120EPDNEW
RGD ID:6857152
Promoter ID:EPDNEW_H1741
Type:initiation region
Name:SMCP_1
Description:sperm mitochondria associated cysteine rich protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H1740  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381152,878,322 - 152,878,382EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:6962 AgrOrtholog
COSMIC SMCP COSMIC
Ensembl Genes ENSG00000163206 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000368765 ENTREZGENE
  ENST00000368765.4 UniProtKB/Swiss-Prot
GTEx ENSG00000163206 GTEx
HGNC ID HGNC:6962 ENTREZGENE
Human Proteome Map SMCP Human Proteome Map
KEGG Report hsa:4184 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 4184 ENTREZGENE
OMIM 601148 OMIM
PANTHER PTHR35820 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPERM MITOCHONDRIAL-ASSOCIATED CYSTEINE-RICH PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA30710 PharmGKB
UniProt MCSP_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q5T7P5 ENTREZGENE, UniProtKB/TrEMBL
  Q96A42 ENTREZGENE
UniProt Secondary Q96A42 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-02 SMCP  sperm mitochondria associated cysteine rich protein  SMCP  sperm mitochondria-associated cysteine-rich protein  Symbol and/or name change 5135510 APPROVED