SSX6P (SSX family member 6, pseudogene) - Rat Genome Database

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Gene: SSX6P (SSX family member 6, pseudogene) Homo sapiens
Analyze
No known orthologs.
Symbol: SSX6P
Name: SSX family member 6, pseudogene
RGD ID: 1353514
HGNC Page HGNC:19652
Description: Predicted to be involved in regulation of DNA-templated transcription. Predicted to be active in nucleus.
Type: pseudo (Ensembl: transcribed_unprocessed_pseudogene)
RefSeq Status: REVIEWED
Previously known as: dJ54B20.1; FLJ53113; psiSSX2; SSX6; SSXP2; synovial sarcoma, X breakpoint 6 (pseudogene)
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Related Functional Gene: SSX5  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X48,107,982 - 48,120,686 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX48,109,981 - 48,119,630 (+)EnsemblGRCh38hg38GRCh38
GRCh37X47,967,367 - 47,980,068 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X47,852,032 - 47,865,013 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X47,723,341 - 47,736,323NCBI
CeleraX52,163,320 - 52,176,024 (+)NCBICelera
Cytogenetic MapXp11.23NCBI
HuRefX45,681,636 - 45,692,386 (+)NCBIHuRef
CHM1_1X47,998,661 - 48,011,372 (+)NCBICHM1_1
T2T-CHM13v2.0X47,518,129 - 47,530,833 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA,IEA)

References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
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:11107170   PMID:12216073   PMID:12477932   PMID:15772651   PMID:17117414   PMID:21873635   PMID:28514442   PMID:30021884   PMID:33961781  


Genomics

Variants

.
Variants in SSX6P
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000050385]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000050385]|See cases [RCV000050385] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x1 copy number loss Global developmental delay [RCV000050386]|See cases [RCV000050386] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:237659-156022362)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052327]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052327]|See cases [RCV000052327] ChrX:237659..156022362 [GRCh38]
ChrX:154326..155252027 [GRCh37]
ChrX:94326..154905221 [NCBI36]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x1 copy number loss Global developmental delay [RCV000052986]|Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052987]|Intellectual functioning disability [RCV000052988]|Global developmental delay [RCV000052989]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052987]|See cases [RCV000052986] ChrX:26102..155996431 [GRCh38]
ChrX:76102..155226096 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:14245-155999293)x1 copy number loss Hypoplastic left heart [RCV000052982]|See cases [RCV000052982] ChrX:14245..155999293 [GRCh38]
ChrX:64245..155228958 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
GRCh38/hg38 Xp22.33-11.21(chrX:10679-55550898)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052971]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052971]|See cases [RCV000052971] ChrX:10679..55550898 [GRCh38]
ChrX:60679..55577331 [GRCh37]
ChrX:679..55594056 [NCBI36]
ChrX:Xp22.33-11.21		 pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x3 copy number gain Global developmental delay [RCV000052984]|Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052985]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052985]|See cases [RCV000052984] ChrX:26102..155996431 [GRCh38]
ChrX:76102..155226096 [GRCh37]
ChrX:Xp22.33-q28		 pathogenic
NR_028366.1(SSX6):n.471G>A single nucleotide variant Malignant melanoma [RCV000073200] ChrX:48117080 [GRCh38]
ChrX:47976462 [GRCh37]
ChrX:47861406 [NCBI36]
ChrX:Xp11.23		 not provided
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x3 copy number gain See cases [RCV000050385] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:679..154896026 [NCBI36]
ChrX:Xp22.33-q28		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:492
Count of miRNA genes:415
Interacting mature miRNAs:448
Transcripts:ENST00000319275, ENST00000376932, ENST00000412590, ENST00000509958
Prediction methods: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 adipose tissue appendage entire extraembryonic component
High
Medium 3 1 1 10 1 1 4 1 1 2
Low 8 13 6 134 7 14 19 15 4 374 35 4 1
Below cutoff 204 203 220 44 259 33 353 136 338 46 207 416 15 152 153 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000376932
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 EnsemblX48,109,981 - 48,119,630 (+)Ensembl
RefSeq Acc Id: ENST00000412590
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 EnsemblX48,107,992 - 48,114,311 (+)Ensembl
RefSeq Acc Id: ENST00000509958
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 EnsemblX48,117,084 - 48,120,210 (+)Ensembl
RefSeq Acc Id: NR_028366
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X48,107,982 - 48,120,686 (+)NCBI
GRCh37X47,967,367 - 47,980,068 (+)RGD
CeleraX52,163,320 - 52,176,024 (+)RGD
HuRefX45,681,636 - 45,692,386 (+)NCBI
CHM1_1X47,998,661 - 48,011,372 (+)NCBI
T2T-CHM13v2.0X47,518,129 - 47,530,833 (+)NCBI
Sequence:
Reference Protein Sequences
Protein Domains
KRAB-related

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7RTT6-F1-model_v2 AlphaFold Q7RTT6 1-188 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:19652 AgrOrtholog
COSMIC SSX6P COSMIC
Ensembl Genes ENSG00000171483 Ensembl
GTEx ENSG00000171483 GTEx
HGNC ID HGNC:19652 ENTREZGENE
Human Proteome Map SSX6P Human Proteome Map
InterPro KRAB UniProtKB/Swiss-Prot
  KRAB_dom_sf UniProtKB/Swiss-Prot
  Krueppel-associated_box-rel UniProtKB/Swiss-Prot
  SSXRD_motif UniProtKB/Swiss-Prot
NCBI Gene 280657 ENTREZGENE
OMIM 300541 OMIM
PANTHER PROTEIN SSX6-RELATED UniProtKB/Swiss-Prot
  PTHR14112 UniProtKB/Swiss-Prot
Pfam SSXRD UniProtKB/Swiss-Prot
PROSITE KRAB_RELATED UniProtKB/Swiss-Prot
SMART KRAB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF109640 UniProtKB/Swiss-Prot
UniProt Q7RTT6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-29 SSX6P  SSX family member 6, pseudogene  SSX6  SSX family member 6, pseudogene  Symbol and/or name change 5135510 APPROVED
2016-05-31 SSX6  SSX family member 6, pseudogene  SSX6  synovial sarcoma, X breakpoint 6 (pseudogene)  Symbol and/or name change 5135510 APPROVED