SLC30A6-DT (SLC30A6 divergent transcript) - Rat Genome Database

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Gene: SLC30A6-DT (SLC30A6 divergent transcript) Homo sapiens
Analyze
Symbol: SLC30A6-DT
Name: SLC30A6 divergent transcript
RGD ID: 39128307
HGNC Page HGNC:55203
Description: ASSOCIATED WITH hereditary spastic paraplegia 4
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38232,165,041 - 32,165,739 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl232,165,041 - 32,165,757 (-)EnsemblGRCh38hg38GRCh38
Cytogenetic Map2p22.3NCBI
T2T-CHM13v2.0232,213,600 - 32,214,298 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3 copy number gain See cases [RCV000141829] Chr2:12770..33711509 [GRCh38]
Chr2:12770..33936576 [GRCh37]
Chr2:2770..33790080 [NCBI36]
Chr2:2p25.3-22.3		 pathogenic
GRCh38/hg38 2p25.3-16.1(chr2:66097-55570637)x3 copy number gain See cases [RCV000052933] Chr2:66097..55570637 [GRCh38]
Chr2:66097..55797773 [GRCh37]
Chr2:56097..55651277 [NCBI36]
Chr2:2p25.3-16.1		 pathogenic
GRCh38/hg38 2p25.3-21(chr2:236816-45983232)x3 copy number gain See cases [RCV000143682] Chr2:236816..45983232 [GRCh38]
Chr2:236816..46210371 [GRCh37]
Chr2:226816..46063875 [NCBI36]
Chr2:2p25.3-21		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203459] Chr2:32147734..32171797 [GRCh38]
Chr2:32372803..32396866 [GRCh37]
Chr2:2p22.3		 pathogenic
GRCh38/hg38 2p22.3(chr2:32107824-32499727)x3 copy number gain See cases [RCV000137454] Chr2:32107824..32499727 [GRCh38]
Chr2:32332893..32724794 [GRCh37]
Chr2:32186397..32578298 [NCBI36]
Chr2:2p22.3		 uncertain significance
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203474] Chr2:32153575..32178196 [GRCh38]
Chr2:32378643..32403264 [GRCh37]
Chr2:2p22.3		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203483] Chr2:32088102..32183850 [GRCh38]
Chr2:32313171..32408919 [GRCh37]
Chr2:2p22.3		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203480] Chr2:32145356..32177032 [GRCh38]
Chr2:32370423..32402099 [GRCh37]
Chr2:2p22.3		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203486] Chr2:32147746..32173488 [GRCh38]
Chr2:32372815..32398557 [GRCh37]
Chr2:2p22.3		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203451] Chr2:32117629..32178282 [GRCh38]
Chr2:32342697..32403350 [GRCh37]
Chr2:2p22.3		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203492] Chr2:32096488..32197021 [GRCh38]
Chr2:32321557..32422090 [GRCh37]
Chr2:2p22.3		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203463] Chr2:32153604..32171983 [GRCh38]
Chr2:32378673..32397052 [GRCh37]
Chr2:2p22.3		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203464] Chr2:32122553..32167306 [GRCh38]
Chr2:32347622..32392375 [GRCh37]
Chr2:2p22.3		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203489] Chr2:32076979..32247094 [GRCh38]
Chr2:32302047..32472162 [GRCh37]
Chr2:2p22.3		 pathogenic
Single allele deletion Hereditary spastic paraplegia 4 [RCV000203469] Chr2:32147763..32165337 [GRCh38]
Chr2:32372832..32390406 [GRCh37]
Chr2:2p22.3		 pathogenic|likely pathogenic
GRCh38/hg38 2p22.3(chr2:32104942-32501212)x3 copy number gain See cases [RCV000141819] Chr2:32104942..32501212 [GRCh38]
Chr2:32330011..32726279 [GRCh37]
Chr2:32183515..32579783 [NCBI36]
Chr2:2p22.3		 uncertain significance
GRCh38/hg38 2p23.1-22.3(chr2:31370181-32512769)x1 copy number loss See cases [RCV000053981] Chr2:31370181..32512769 [GRCh38]
Chr2:31593047..32737836 [GRCh37]
Chr2:31446551..32591340 [NCBI36]
Chr2:2p23.1-22.3		 pathogenic
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2		 benign

Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENST00000608489
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl232,165,041 - 32,165,757 (-)Ensembl
RefSeq Acc Id: NR_185886
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38232,165,041 - 32,165,739 (-)NCBI
T2T-CHM13v2.0232,213,600 - 32,214,298 (-)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC SLC30A6-DT COSMIC
Ensembl Genes ENSG00000272716 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000608489 ENTREZGENE
GTEx ENSG00000272716 GTEx
HGNC ID HGNC:55203 ENTREZGENE
Human Proteome Map SLC30A6-DT Human Proteome Map
NCBI Gene SLC30A6-DT ENTREZGENE
RNAcentral URS00026A22BC RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-05-31 SLC30A6-DT  SLC30A6 divergent transcript  SLC30A6-DT  SLC30A6 divergent transcript  Data merged from RGD:16566515 737654 PROVISIONAL
2020-08-24 SLC30A6-DT  SLC30A6 divergent transcript  AL121658.1  novel transcript  Symbol and/or name change 19259463 PROVISIONAL