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Analyze GeneStrainQTL List |
 Gene Annotator (Functional Annotation) unavailable |
 Gene Annotator (Annotation Distribution) unavailable |
 Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable |
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 InterViewer (Protein-Protein Interactions) unavailable |
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 Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable |
InterViewer (Protein-Protein Interactions) |
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 Gene Annotator (Annotation Comparison) unavailable |
 OLGA (Gene List Generator) unavailable |
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Gene Annotator (Annotation Comparison) |
OLGA (Gene List Generator) |
Excel (Download) |
 MOET (Multi-Ontology Enrichement) unavailable |
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MOET (Multi-Ontology Enrichement) |
GOLF (Gene-Ortholog Location Finder) |
Imported Annotations - ClinVar | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Term | Qualifier | Evidence | With | Reference | Notes | Source | Original Reference(s) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| long QT syndrome | IAGP | RGD:10395414 | 8554872 | ClinVar Annotator: match by term: Long QT syndrome | ClinVar | PMID:26132555 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene-Chemical Interaction AnnotationsGene Ontology AnnotationsMolecular Pathway AnnotationsDisease Annotations
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Gene-Chemical Interaction Annotations
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Gene Ontology Annotations
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Molecular Pathway AnnotationsReferences - curated| 1. | Bjornson Granqvist A, etal., Am J Physiol Renal Physiol. 2006 Oct;291(4):F722-30. Epub 2006 Apr 18. |
| 2. | Carbone A, etal., Blood. 1998 Oct 1;92(7):2220-8. |
| 3. | Carbone A, etal., Blood. 2001 Feb 1;97(3):744-51. |
| 4. | Cortes V, etal., Liver Int. 2007 May;27(4):569-81. |
| 5. | Endo C, etal., Coron Artery Dis. 1997 Mar-Apr;8(3-4):155-61. |
| 6. | Gharagozlian S, etal., Eur J Nutr. 2006 Oct;45(7):369-75. Epub 2006 Jun 29. |
| 7. | GOA_HUMAN data from the GO Consortium |
| 8. | Mulivor AW and Lipowsky HH, Am J Physiol Heart Circ Physiol. 2004 May;286(5):H1672-80. Epub 2004 Jan 2. |
| 9. | Olsson U, etal., Diabetes. 2001 Sep;50(9):2126-32. |
| 10. | Pipeline to import KEGG annotations from KEGG into RGD |
| 11. | Pipeline to import Pathway Interaction Database annotations from NCI into RGD |
| 12. | RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations |
| 13. | RGD automated import pipeline for gene-chemical interactions |
| 14. | Seeley RJ, etal., Annu Rev Nutr 2004;24:133-49. |
References - uncurated| PubMed | 1339431 1442271 1644217 1664683 2173154 2324102 2519615 7592855 7592967 7690138 7959737 8118875 8125298 8163535 8570206 8889548 9050911 9089390 9111037 9294130 9342064 9548182 9565572 9566955 9660868 9792716 9857223 10497173 10506830 11024024 11168765 11179419 11567105 11830493 11877089 12091355 12144130 12464176 12477932 12660231 12749851 12824007 12879463 12885232 12902511 12904296 12920224 12947106 12975379 14521955 14630925 14637022 14645569 14701864 14744776 14972511 15126321 15292202 15297422 15383330 15459490 15479743 15489334 15648090 15728209 15743035 15770719 15797855 15886501 15902740 16007225 16020957 16132527 16157597 16247452 16286510 16341674 16636895 16720645 16773719 16778379 16817962 16840194 16857657 16884912 16934308 16945147 16982797 17149710 17314405 17339423 17413980 17431390 17455248 17579341 17625591 18006945 18029348 18064305 18093920 18190591 18378436 18386024 18413760 18450428 18450755 18542065 18657535 18694404 18957427 18976975 18997617 19010933 19020713 19029267 19056867 19073610 19107206 19126645 19228696 19251947 19255147 19305494 19351365 19420730 19450993 19456850 19473447 19581738 19596856 19632304 19661268 19696445 19735958 19802384 19822079 19859083 19860843 19866343 19875451 20008145 20013319 20036233 20081059 20083849 20097882 20181947 20193112 20200931 20204274 20237901 20307537 20361982 20398359 20430722 20471559 20477813 20598296 20683626 20736897 20927321 20971705 21114861 21148276 21257720 21265098 21317913 21320038 21327984 21334435 21414405 21430259 21454203 21463121 21623993 21630196 21731601 21757697 21772125 21832049 21873635 21886795 21898481 21957484 22024722 22102278 22150439 22237752 22238310 22298773 22308310 22338054 22351752 22418956 22573479 22629140 22660413 22672327 22673509 22680042 22686587 22714920 22745764 22766978 22899717 22905270 22936802 22939629 22994707 23066085 23144729 23206733 23289672 23331867 23395182 23408834 23431957 23504321 23511033 23545927 23546957 23553620 23570784 23576506 23728345 23729443 23824909 23888783 23988031 23991032 24029663 24045542 24145151 24222257 24283919 24388357 24392029 24424718 24524203 24529757 24549646 24656090 24751902 24762495 24956062 24957789 24970903 24982376 25017879 25063885 25115297 25120060 25147801 25198673 25202019 25236603 25267953 25273930 25274915 25321193 25344834 25353275 25361632 25404732 25462564 25512478 25589885 25662098 25732677 25757215 25830352 25891890 25972509 26057450 26076711 26191180 26210886 26259043 26289843 26350464 26460958 26513873 26514209 26526579 26561776 26729247 26852939 26909794 26953518 26972718 27299886 27305940 27434331 27472156 27556509 27578500 27758044 27819680 27838471 27930836 28077445 28107214 28270211 28351285 28382590 28514442 28574293 28579548 28585128 28843664 29212806 29216821 29355516 29467282 29484435 29509190 29601451 29628317 29798960 29850393 29936329 29956739 29976229 30065348 30151336 30275097 30379102 30578753 30639242 30738694 30918400 31145753 |
Candidate Gene StatusComparative Map Data| SDC1 (Homo sapiens - human) |
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| Sdc1 (Mus musculus - house mouse) |
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| Sdc1 (Rattus norvegicus - Norway rat) |
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| Sdc1 (Chinchilla lanigera - long-tailed chinchilla) |
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| SDC1 (Pan paniscus - bonobo/pygmy chimpanzee) |
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| SDC1 (Canis lupus familiaris - dog) |
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| Sdc1 (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| SDC1 (Sus scrofa - pig) |
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| SDC1 (Chlorocebus sabaeus - green monkey) |
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| Sdc1 (Heterocephalus glaber - naked mole-rat) |
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Position Markers| RH67771 |
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| RH16622 |
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| RH17406 |
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miRNA Target Status
| 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. |
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RNA-SEQ Expression| uterine cervix | peripheral nervous system | zone of skin | lymph node | large intestine | oral cavity | blood | breast | throat | mucosa | prefrontal cortex | testis | stomach | heart | brain | cerebral cortex | eye | pleura | penis | ovary | uterus | vagina | mammalian vulva | seminal vesicle | vas deferens | adipose tissue | musculature | chordate pharynx | esophagus | saliva-secreting gland | rectum | skeletal muscle tissue | smooth muscle tissue | caecum | vermiform appendix | colon | sigmoid colon | renal pelvis | cortex of kidney | urinary bladder | pancreas | endometrium | epididymis | muscle of leg | muscle of arm | nasal septum | tongue | submandibular gland | skeletal muscle of trunk | parotid gland | temporal lobe | forebrain | placenta | hindbrain | epithelium of bronchus | cerebellum | substantia nigra | thyroid gland | lung | spleen | liver | small intestine | gall bladder | kidney | duodenum | ileum | spinal cord | umbilical cord | dura mater | prostate gland | adrenal gland | thymus | bone marrow | tonsil | connective tissue | hematopoietic system | bile duct | cartilage tissue | bone tissue | trachea | mouth mucosa | fallopian tube | left kidney | umbilical cord blood | venous blood | frontal lobe | left renal pelvis | right renal pelvis | distal gut | proximal gut | terminal ileum | |
| High | 4 | 3 | 7 | 3 | 1 | 2 | 21 | 5 | 1 | 25 | 4 | 23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Medium | 35 | 12 | 274 | 2 | 87 | 4 | 203 | 161 | 29 | 21 | 65 | 4 | 80 | 3 | 172 | 49 | 3 | 1 | 2 | 2 | 32 | 1 | 2 | 1 | 2 | 1 | 42 | 1 | 1 | 1 | 16 | 105 | 1 | 1 | 8 | 10 | 4 | 11 | 1 | 1 | 60 | 279 | 1 | 227 | 3 | 3 | 258 | 1 | 1 | 1 | 27 | 6 | 2 | 2 | 6 | 23 | 2 | 2 | 24 | 20 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ||||||||||||||||||||||||
| Low | 2 | 4 | 26 | 12 | 1 | 313 | 1 | 1 | 1 | 7 | 4 | 13 | 30 | 1 | 1 | 1 | 9 | 3 | 1 | 1 | 1 | 2 | 2 | 1 | 1 | 1 | 1 | 4 | 1 | 2 | 3 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 10 | 1 | 1 | 6 | 1 | 2 | 1 | 1 | 7 | 1 | 1 | 1 | 2 | 1 | 2 | 26 | 19 | 1 | 2 | 1 | 1 | |||||||||||||||||||||||||||||||
| Below cutoff | 1 | 2 | 9 | 61 | 8 | 1 | 1 | 1 | 1 | 1 | 3 | 17 | 2 |
Nucleotide Sequences| RefSeq Transcripts | NG_050639 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| NM_001006946 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| NM_002997 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_005262620 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_005262621 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| XM_005262622 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| GenBank Nucleotide | AC104792 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AJ551176 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AK222739 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AK299385 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AK307313 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AK311409 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AK313974 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BC008765 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BM785035 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BM910157 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CB321970 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CH471053 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| J05392 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| KT583891 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| X60306 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| Z48199 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| RefSeq Acc Id: | NM_001006946 ⟹ NP_001006947 | |||||||||||||||||||||||||||||
| RefSeq Status: | REVIEWED | |||||||||||||||||||||||||||||
| Type: | CODING | |||||||||||||||||||||||||||||
| Position: |
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| Sequence: |
TTCAGCCCCTCTCCCGGGCTGCGCCTCCGCACTCCGGGCCCGGGCAGAAGGGGGTGCGCCTCGGhide sequence |
| RefSeq Acc Id: | NM_002997 ⟹ NP_002988 | |||||||||||||||||||||||||||||
| RefSeq Status: | REVIEWED | |||||||||||||||||||||||||||||
| Type: | CODING | |||||||||||||||||||||||||||||
| Position: |
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| Sequence: |
GGCCGGGAGACCTGGCGGAGCTGGGGGTGGGGGGCCAGTTTTTGCAACGGCTAAGGAAGGGCCThide sequence |
| RefSeq Acc Id: | XM_005262620 ⟹ XP_005262677 | ||||||||||||||
| RefSeq Status: | |||||||||||||||
| Type: | CODING | ||||||||||||||
| Position: |
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| Sequence: |
GTTGCCTCATTGTTGAATGGAGCATGGATCCAATGGTTCTAGCTTCTGCTGAAAGATTCGGCAChide sequence |
| RefSeq Acc Id: | XM_005262621 ⟹ XP_005262678 | ||||||||||||||
| RefSeq Status: | |||||||||||||||
| Type: | CODING | ||||||||||||||
| Position: |
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| Sequence: |
GGGATTACAGGCGTGAGCCACTGCACCAGTCAAGTCAATGACTGTTTATTGTAGATGGGCCATGhide sequence |
| RefSeq Acc Id: | XM_005262622 ⟹ XP_005262679 | ||||||||||||||
| RefSeq Status: | |||||||||||||||
| Type: | CODING | ||||||||||||||
| Position: |
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| Sequence: |
TACAGAGTCTGTCTCATGGGAGATGAGCAAATTGTGGCTACTAATTTGCCCCCTGAAGATCAAGhide sequence |
Protein Sequences| Protein RefSeqs | NP_001006947 | (Get FASTA) | NCBI Sequence Viewer |
| NP_002988 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_005262677 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_005262678 | (Get FASTA) | NCBI Sequence Viewer | |
| XP_005262679 | (Get FASTA) | NCBI Sequence Viewer | |
| GenBank Protein | AAA60605 | (Get FASTA) | NCBI Sequence Viewer |
| AAH08765 | (Get FASTA) | NCBI Sequence Viewer | |
| AAX93151 | (Get FASTA) | NCBI Sequence Viewer | |
| BAD96459 | (Get FASTA) | NCBI Sequence Viewer | |
| BAG61371 | (Get FASTA) | NCBI Sequence Viewer | |
| CAA42851 | (Get FASTA) | NCBI Sequence Viewer | |
| CAA88235 | (Get FASTA) | NCBI Sequence Viewer | |
| CAD80245 | (Get FASTA) | NCBI Sequence Viewer | |
| EAX00828 | (Get FASTA) | NCBI Sequence Viewer | |
| EAX00829 | (Get FASTA) | NCBI Sequence Viewer | |
| EAX00830 | (Get FASTA) | NCBI Sequence Viewer | |
| EAX00831 | (Get FASTA) | NCBI Sequence Viewer | |
| P18827 | (Get FASTA) | NCBI Sequence Viewer |
| RefSeq Acc Id: | NP_001006947 ⟸ NM_001006946 |
| - Peptide Label: | precursor |
| - UniProtKB: | P18827 (UniProtKB/Swiss-Prot) |
| - Sequence: |
MRRAALWLWLCALALSLQPALPQIVATNLPPEDQDGSGDDSDNFSGSGAGALQDITLSQQTPSThide sequence |
| RefSeq Acc Id: | NP_002988 ⟸ NM_002997 |
| - Peptide Label: | precursor |
| - Sequence: |
MRRAALWLWLCALALSLQPALPQIVATNLPPEDQDGSGDDSDNFSGSGAGALQDITLSQQTPSThide sequence |
| RefSeq Acc Id: | XP_005262679 ⟸ XM_005262622 |
| - Peptide Label: | isoform X3 |
| - Sequence: |
MGDEQIVATNLPPEDQDGSGDDSDNFSGSGAGALQDITLSQQTPSTWKDTQLLTAIPTSPEPTGhide sequence |
| RefSeq Acc Id: | XP_005262677 ⟸ XM_005262620 |
| - Peptide Label: | isoform X1 |
| - Sequence: |
MQQRLVGSKCQCLAPSLPHLELSLGGGGAAGEGRAESLDESEAMIPQIVATNLPPEDQDGSGDDhide sequence |
| RefSeq Acc Id: | XP_005262678 ⟸ XM_005262621 |
| - Peptide Label: | isoform X2 |
| - Sequence: |
MTVYCRWAMVDCDCSLQQIVATNLPPEDQDGSGDDSDNFSGSGAGALQDITLSQQTPSTWKDTQhide sequence |
Promoters| RGD ID: | 6859716 | |||||||||
| Promoter ID: | EPDNEW_H3022 | |||||||||
| Type: | initiation region | |||||||||
| Name: | SDC1_1 | |||||||||
| Description: | syndecan 1 | |||||||||
| SO ACC ID: | SO:0000170 | |||||||||
| Source: | EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/) | |||||||||
| Alternative Promoters: | null; see alsoEPDNEW_H3023 | |||||||||
| Experiment Methods: | Single-end sequencing. | |||||||||
| Position: |
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| RGD ID: | 6859718 | |||||||||
| Promoter ID: | EPDNEW_H3023 | |||||||||
| Type: | initiation region | |||||||||
| Name: | SDC1_2 | |||||||||
| Description: | syndecan 1 | |||||||||
| SO ACC ID: | SO:0000170 | |||||||||
| Source: | EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/) | |||||||||
| Alternative Promoters: | null; see alsoEPDNEW_H3022 | |||||||||
| Experiment Methods: | Single-end sequencing.; Paired-end sequencing. | |||||||||
| Position: |
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| RGD ID: | 6798146 | |||||||||
| Promoter ID: | HG_KWN:31674 | |||||||||
| Type: | CpG-Island | |||||||||
| SO ACC ID: | SO:0000170 | |||||||||
| Source: | MPROMDB | |||||||||
| Tissues & Cell Lines: | K562, Lymphoblastoid, NB4 | |||||||||
| Transcripts: | OTTHUMT00000323932, UC010EXW.1 | |||||||||
| Position: |
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| RGD ID: | 6798126 | |||||||||
| Promoter ID: | HG_KWN:31675 | |||||||||
| Type: | CpG-Island | |||||||||
| SO ACC ID: | SO:0000170 | |||||||||
| Source: | MPROMDB | |||||||||
| Tissues & Cell Lines: | HeLa_S3, K562, Lymphoblastoid | |||||||||
| Transcripts: | OTTHUMT00000323934 | |||||||||
| Position: |
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| RGD ID: | 6798125 | |||||||||
| Promoter ID: | HG_KWN:31676 | |||||||||
| Type: | CpG-Island | |||||||||
| SO ACC ID: | SO:0000170 | |||||||||
| Source: | MPROMDB | |||||||||
| Tissues & Cell Lines: | HeLa_S3, Lymphoblastoid, NB4 | |||||||||
| Transcripts: | NM_001006946, NM_002997, OTTHUMT00000323933, UC010EXV.1 | |||||||||
| Position: |
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| RGD ID: | 6853472 | |||||||||
| Promoter ID: | EP74561 | |||||||||
| Type: | initiation region | |||||||||
| Name: | HS_SDC1 | |||||||||
| Description: | Syndecan 1. | |||||||||
| 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: |
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Clinical Variants| Name | Type | Condition(s) | Position(s) | Clinical significance |
| GRCh38/hg38 2p25.3-23.1(chr2:30141-31766749)x3 | copy number gain | Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052929]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052929]|See cases [RCV000052929] | Chr2:30141..31766749 [GRCh38] Chr2:30141..31991818 [GRCh37] Chr2:20141..31845322 [NCBI36] Chr2:2p25.3-23.1 |
pathogenic |
| GRCh38/hg38 2p25.3-16.1(chr2:66097-55570637)x3 | copy number gain | Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052933]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052933]|See cases [RCV000052933] | Chr2:66097..55570637 [GRCh38] Chr2:66097..55797773 [GRCh37] Chr2:56097..55651277 [NCBI36] Chr2:2p25.3-16.1 |
pathogenic |
| NM_001006946.1(SDC1):c.929C>T (p.Ala310Val) | single nucleotide variant | Malignant melanoma [RCV000065364] | Chr2:20202770 [GRCh38] Chr2:20402531 [GRCh37] Chr2:20266012 [NCBI36] Chr2:2p24.1 |
not provided |
| NM_001006946.1(SDC1):c.439G>A (p.Glu147Lys) | single nucleotide variant | Malignant melanoma [RCV000065366] | Chr2:20204001 [GRCh38] Chr2:20403762 [GRCh37] Chr2:20267243 [NCBI36] Chr2:2p24.1 |
not provided |
| NM_001006946.1(SDC1):c.709C>T (p.Gln237Ter) | single nucleotide variant | Malignant melanoma [RCV000060460] | Chr2:20203141 [GRCh38] Chr2:20402902 [GRCh37] Chr2:20266383 [NCBI36] Chr2:2p24.1 |
not provided |
| GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3 | copy number gain | See cases [RCV000135398] | Chr2:30341..28419664 [GRCh38] Chr2:30341..28642531 [GRCh37] Chr2:20341..28496035 [NCBI36] Chr2:2p25.3-23.2 |
pathogenic |
| GRCh38/hg38 2p25.3-23.3(chr2:17019-26318846)x3 | copy number gain | See cases [RCV000137344] | Chr2:17019..26318846 [GRCh38] Chr2:17019..26541714 [GRCh37] Chr2:7019..26395218 [NCBI36] Chr2:2p25.3-23.3 |
pathogenic |
| GRCh38/hg38 2p25.3-24.1(chr2:1664615-23664142)x3 | copy number gain | See cases [RCV000137913] | Chr2:1664615..23664142 [GRCh38] Chr2:1668387..23887012 [GRCh37] Chr2:1647394..23740517 [NCBI36] Chr2:2p25.3-24.1 |
pathogenic|likely pathogenic |
| GRCh38/hg38 2p24.2-24.1(chr2:16723596-21600734)x1 | copy number loss | See cases [RCV000139451] | Chr2:16723596..21600734 [GRCh38] Chr2:16904863..21823606 [GRCh37] Chr2:16768344..21677111 [NCBI36] Chr2:2p24.2-24.1 |
pathogenic|likely pathogenic |
| 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 2p25.3-23.3(chr2:12770-25039694)x3 | copy number gain | See cases [RCV000141877] | Chr2:12770..25039694 [GRCh38] Chr2:12770..25262563 [GRCh37] Chr2:2770..25116067 [NCBI36] Chr2:2p25.3-23.3 |
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 |
| 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 |
| NM_002997.5(SDC1):c.188C>T (p.Ser63Phe) | single nucleotide variant | Long QT syndrome [RCV000190182] | Chr2:20204252 [GRCh38] Chr2:20404013 [GRCh37] Chr2:2p24.1 |
likely benign |
| GRCh37/hg19 2p24.1(chr2:20423601-20425165)x1 | copy number loss | not provided [RCV000752873] | Chr2:20423601..20425165 [GRCh37] Chr2:2p24.1 |
benign |
| GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384) | copy number gain | See cases [RCV000512056] | Chr2:12771..242783384 [GRCh37] Chr2:2p25.3-q37.3 |
pathogenic |
| GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3 | copy number gain | See cases [RCV000511212] | Chr2:12771..242783384 [GRCh37] Chr2:2p25.3-q37.3 |
pathogenic |
| GRCh37/hg19 2p24.1-23.3(chr2:19905995-24762790)x1 | copy number loss | not provided [RCV000682157] | Chr2:19905995..24762790 [GRCh37] Chr2:2p24.1-23.3 |
pathogenic |
| GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3 | copy number gain | not provided [RCV000752804] | Chr2:15672..243101834 [GRCh37] Chr2:2p25.3-q37.3 |
pathogenic |
| GRCh37/hg19 2p24.1(chr2:20423601-20424725)x1 | copy number loss | not provided [RCV000752871] | Chr2:20423601..20424725 [GRCh37] Chr2:2p24.1 |
benign |
| GRCh37/hg19 2p24.1(chr2:20423867-20427189)x1 | copy number loss | not provided [RCV000752874] | Chr2:20423867..20427189 [GRCh37] Chr2:2p24.1 |
benign |
| GRCh37/hg19 2p24.1(chr2:20423488-20424838)x1 | copy number loss | not provided [RCV000752870] | Chr2:20423488..20424838 [GRCh37] Chr2:2p24.1 |
benign |
| GRCh37/hg19 2p24.1(chr2:20423601-20424838)x1 | copy number loss | not provided [RCV000752872] | Chr2:20423601..20424838 [GRCh37] Chr2:2p24.1 |
benign |
| GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3 | copy number gain | not provided [RCV000752802] | Chr2:14238..243048760 [GRCh37] Chr2:2p25.3-q37.3 |
pathogenic |
| GRCh37/hg19 2p24.1(chr2:20423264-20425165)x0 | copy number loss | not provided [RCV000752868] | Chr2:20423264..20425165 [GRCh37] Chr2:2p24.1 |
benign |
| GRCh37/hg19 2p24.1(chr2:20423488-20424725)x1 | copy number loss | not provided [RCV000752869] | Chr2:20423488..20424725 [GRCh37] Chr2:2p24.1 |
benign |
| GRCh37/hg19 2p24.1(chr2:20421008-20430049)x1 | copy number loss | not provided [RCV000740350] | Chr2:20421008..20430049 [GRCh37] Chr2:2p24.1 |
benign |
| NM_002997.5(SDC1):c.672C>T (p.Ala224=) | single nucleotide variant | not provided [RCV000904725] | Chr2:20203178 [GRCh38] Chr2:20402939 [GRCh37] Chr2:2p24.1 |
likely benign |
| NM_002997.5(SDC1):c.576T>C (p.Ala192=) | single nucleotide variant | not provided [RCV000768080] | Chr2:20203864 [GRCh38] Chr2:20403625 [GRCh37] Chr2:2p24.1 |
uncertain significance |
| NM_002997.5(SDC1):c.203C>T (p.Thr68Met) | single nucleotide variant | not provided [RCV000973667] | Chr2:20204237 [GRCh38] Chr2:20403998 [GRCh37] Chr2:2p24.1 |
benign |
| NM_002997.5(SDC1):c.346G>A (p.Ala116Thr) | single nucleotide variant | not provided [RCV000918508] | Chr2:20204094 [GRCh38] Chr2:20403855 [GRCh37] Chr2:2p24.1 |
benign |
| NM_002997.5(SDC1):c.227C>T (p.Thr76Met) | single nucleotide variant | not provided [RCV000894306] | Chr2:20204213 [GRCh38] Chr2:20403974 [GRCh37] Chr2:2p24.1 |
benign |
| GRCh37/hg19 2p24.3-24.1(chr2:15631145-21729493)x1 | copy number loss | not provided [RCV000847885] | Chr2:15631145..21729493 [GRCh37] Chr2:2p24.3-24.1 |
pathogenic |
| GRCh37/hg19 2p24.1(chr2:20167711-20601004)x3 | copy number gain | not provided [RCV000848211] | Chr2:20167711..20601004 [GRCh37] Chr2:2p24.1 |
uncertain significance |
| NM_002997.5(SDC1):c.312T>C (p.Ala104=) | single nucleotide variant | not provided [RCV000952820] | Chr2:20204128 [GRCh38] Chr2:20403889 [GRCh37] Chr2:2p24.1 |
benign |
| NM_002997.5(SDC1):c.244G>A (p.Gly82Ser) | single nucleotide variant | not provided [RCV000888906] | Chr2:20204196 [GRCh38] Chr2:20403957 [GRCh37] Chr2:2p24.1 |
benign |
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | HGNC:10658 | AgrOrtholog |
| COSMIC | SDC1 | COSMIC |
| Ensembl Genes | ENSG00000115884 | Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot |
| Ensembl Protein | ENSP00000254351 | ENTREZGENE, UniProtKB/Swiss-Prot |
| ENSP00000370542 | ENTREZGENE, UniProtKB/Swiss-Prot | |
| ENSP00000384613 | UniProtKB/TrEMBL | |
| ENSP00000390201 | UniProtKB/TrEMBL | |
| ENSP00000400773 | UniProtKB/TrEMBL | |
| Ensembl Transcript | ENST00000254351 | ENTREZGENE, UniProtKB/Swiss-Prot |
| ENST00000381150 | ENTREZGENE, UniProtKB/Swiss-Prot | |
| ENST00000403076 | UniProtKB/TrEMBL | |
| ENST00000429035 | UniProtKB/TrEMBL | |
| ENST00000447124 | UniProtKB/TrEMBL | |
| GTEx | ENSG00000115884 | GTEx |
| HGNC ID | HGNC:10658 | ENTREZGENE |
| Human Proteome Map | SDC1 | Human Proteome Map |
| InterPro | Neurexin-like | UniProtKB/Swiss-Prot |
| Syndecan | UniProtKB/Swiss-Prot | |
| Syndecan-1 | UniProtKB/Swiss-Prot | |
| Syndecan/Neurexin_dom | UniProtKB/Swiss-Prot | |
| Syndecan_CS | UniProtKB/Swiss-Prot | |
| KEGG Report | hsa:6382 | UniProtKB/Swiss-Prot |
| NCBI Gene | 6382 | ENTREZGENE |
| OMIM | 186355 | OMIM |
| PANTHER | PTHR10915 | UniProtKB/Swiss-Prot |
| PTHR10915:SF5 | UniProtKB/Swiss-Prot | |
| Pfam | Syndecan | UniProtKB/Swiss-Prot |
| PharmGKB | PA35588 | PharmGKB |
| PROSITE | SYNDECAN | UniProtKB/Swiss-Prot |
| SMART | 4.1m | UniProtKB/Swiss-Prot |
| UniGene | Hs.224607 | ENTREZGENE |
| Hs.665958 | ENTREZGENE | |
| UniProt | E9PHH3_HUMAN | UniProtKB/TrEMBL |
| F8WCX9_HUMAN | UniProtKB/TrEMBL | |
| H7C1K4_HUMAN | UniProtKB/TrEMBL | |
| P18827 | ENTREZGENE, UniProtKB/Swiss-Prot | |
| UniProt Secondary | D6W523 | UniProtKB/Swiss-Prot |
| Q53QV0 | UniProtKB/Swiss-Prot | |
| Q546D3 | UniProtKB/Swiss-Prot | |
| Q96HB7 | UniProtKB/Swiss-Prot |
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| More on SDC1 | |
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Alliance Gene |
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NCBI Gene |
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Ensembl Gene |
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JBrowse: hg19 hg38 |
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HGNC Report |
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NCBI Genome Data Viewer |
| RGD Object Information | |
| RGD ID: | 730864 |
| Created: | 2003-12-10 |
| Species: | Homo sapiens |
| Last Modified: | 2020-02-11 |
| Status: | ACTIVE |
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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.
