LOC130004408 (ATAC-STARR-seq lymphoblastoid active region 3801) - Rat Genome Database

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Gene: LOC130004408 (ATAC-STARR-seq lymphoblastoid active region 3801) Homo sapiens
Analyze
Symbol: LOC130004408
Name: ATAC-STARR-seq lymphoblastoid active region 3801
RGD ID: 329830044
Description: This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381095,693,632 - 95,693,911 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.01096,572,739 - 96,573,018 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC130004408
64 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_015631.6(TCTN3):c.224C>T (p.Ala75Val) single nucleotide variant Orofacial-digital syndrome IV [RCV001085868]|not provided [RCV000430026]|not specified [RCV000194963] Chr10:95693676 [GRCh38]
Chr10:97453433 [GRCh37]
Chr10:10q24.1		 benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_015631.6(TCTN3):c.159G>A (p.Ala53=) single nucleotide variant Orofacial-digital syndrome IV [RCV002059904]|not specified [RCV000431492] Chr10:95693741 [GRCh38]
Chr10:97453498 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.2T>G (p.Met1Arg) single nucleotide variant Joubert syndrome and related disorders [RCV003323961]|Orofacial-digital syndrome IV [RCV001941559]|TCTN3-related condition [RCV003426266] Chr10:95693898 [GRCh38]
Chr10:97453655 [GRCh37]
Chr10:10q24.1		 pathogenic|likely pathogenic
NM_015631.6(TCTN3):c.144G>C (p.Gln48His) single nucleotide variant not specified [RCV001820568] Chr10:95693756 [GRCh38]
Chr10:97453513 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.62G>T (p.Arg21Leu) single nucleotide variant Orofacial-digital syndrome IV [RCV001907752] Chr10:95693838 [GRCh38]
Chr10:97453595 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.11C>T (p.Pro4Leu) single nucleotide variant Orofacial-digital syndrome IV [RCV001935197] Chr10:95693889 [GRCh38]
Chr10:97453646 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.193A>C (p.Thr65Pro) single nucleotide variant Orofacial-digital syndrome IV [RCV001518171]|not specified [RCV000118617] Chr10:95693707 [GRCh38]
Chr10:97453464 [GRCh37]
Chr10:10q24.1		 benign|likely benign|conflicting interpretations of pathogenicity
NM_015631.6(TCTN3):c.222G>A (p.Ser74=) single nucleotide variant Orofacial-digital syndrome IV [RCV001943635] Chr10:95693678 [GRCh38]
Chr10:97453435 [GRCh37]
Chr10:10q24.1		 likely benign|uncertain significance
NM_015631.6(TCTN3):c.194C>T (p.Thr65Ile) single nucleotide variant Orofacial-digital syndrome IV [RCV002041295] Chr10:95693706 [GRCh38]
Chr10:97453463 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.52G>A (p.Asp18Asn) single nucleotide variant Orofacial-digital syndrome IV [RCV002030500] Chr10:95693848 [GRCh38]
Chr10:97453605 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.121G>A (p.Gly41Arg) single nucleotide variant Orofacial-digital syndrome IV [RCV001948069] Chr10:95693779 [GRCh38]
Chr10:97453536 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.178G>A (p.Val60Met) single nucleotide variant Inborn genetic diseases [RCV004045504]|Orofacial-digital syndrome IV [RCV001992007] Chr10:95693722 [GRCh38]
Chr10:97453479 [GRCh37]
Chr10:10q24.1		 likely benign|uncertain significance
GRCh38/hg38 10q23.33-25.3(chr10:95112607-116776637)x3 copy number gain See cases [RCV000050747] Chr10:95112607..116776637 [GRCh38]
Chr10:96872364..118383651 [GRCh37]
Chr10:96862354..118526138 [NCBI36]
Chr10:10q23.33-25.3		 pathogenic
NM_015631.6(TCTN3):c.223G>A (p.Ala75Thr) single nucleotide variant Inborn genetic diseases [RCV002548181]|Orofacial-digital syndrome IV [RCV002014373] Chr10:95693677 [GRCh38]
Chr10:97453434 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.119G>A (p.Arg40Gln) single nucleotide variant Orofacial-digital syndrome IV [RCV001959226] Chr10:95693781 [GRCh38]
Chr10:97453538 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.182dup (p.Gly62fs) duplication Orofacial-digital syndrome IV [RCV002007314] Chr10:95693717..95693718 [GRCh38]
Chr10:97453474..97453475 [GRCh37]
Chr10:10q24.1		 pathogenic
NM_015631.6(TCTN3):c.41T>C (p.Leu14Pro) single nucleotide variant not provided [RCV001758039] Chr10:95693859 [GRCh38]
Chr10:97453616 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.43G>T (p.Val15Leu) single nucleotide variant not provided [RCV001761264] Chr10:95693857 [GRCh38]
Chr10:97453614 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.27G>T (p.Leu9=) single nucleotide variant Orofacial-digital syndrome IV [RCV002157270] Chr10:95693873 [GRCh38]
Chr10:97453630 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.36C>G (p.Phe12Leu) single nucleotide variant not provided [RCV001764054] Chr10:95693864 [GRCh38]
Chr10:97453621 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.245A>T (p.Asp82Val) single nucleotide variant Orofacial-digital syndrome IV [RCV001968011] Chr10:95693655 [GRCh38]
Chr10:97453412 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.28C>A (p.Gln10Lys) single nucleotide variant Inborn genetic diseases [RCV002722740] Chr10:95693872 [GRCh38]
Chr10:97453629 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.57C>T (p.Gly19=) single nucleotide variant Orofacial-digital syndrome IV [RCV002834136] Chr10:95693843 [GRCh38]
Chr10:97453600 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.17T>C (p.Leu6Pro) single nucleotide variant Orofacial-digital syndrome IV [RCV002796816] Chr10:95693883 [GRCh38]
Chr10:97453640 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.18C>G (p.Leu6=) single nucleotide variant Orofacial-digital syndrome IV [RCV002131378] Chr10:95693882 [GRCh38]
Chr10:97453639 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.138C>T (p.Thr46=) single nucleotide variant Orofacial-digital syndrome IV [RCV002090273] Chr10:95693762 [GRCh38]
Chr10:97453519 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.16C>G (p.Leu6Val) single nucleotide variant Orofacial-digital syndrome IV [RCV001867042] Chr10:95693884 [GRCh38]
Chr10:97453641 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.27G>A (p.Leu9=) single nucleotide variant Orofacial-digital syndrome IV [RCV002111592] Chr10:95693873 [GRCh38]
Chr10:97453630 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.137C>T (p.Thr46Ile) single nucleotide variant Orofacial-digital syndrome IV [RCV003016334] Chr10:95693763 [GRCh38]
Chr10:97453520 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.162T>C (p.Thr54=) single nucleotide variant Orofacial-digital syndrome IV [RCV002912590] Chr10:95693738 [GRCh38]
Chr10:97453495 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.6C>A (p.Arg2=) single nucleotide variant Orofacial-digital syndrome IV [RCV002876229] Chr10:95693894 [GRCh38]
Chr10:97453651 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.101C>A (p.Thr34Lys) single nucleotide variant Orofacial-digital syndrome IV [RCV003046589] Chr10:95693799 [GRCh38]
Chr10:97453556 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.152C>A (p.Ser51Ter) single nucleotide variant Long QT syndrome [RCV000190128] Chr10:95693748 [GRCh38]
Chr10:97453505 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.25C>T (p.Leu9=) single nucleotide variant Orofacial-digital syndrome IV [RCV003060909] Chr10:95693875 [GRCh38]
Chr10:97453632 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.3G>A (p.Met1Ile) single nucleotide variant Joubert syndrome 18 [RCV000201547]|Orofacial-digital syndrome IV [RCV000796275]|not provided [RCV003227713] Chr10:95693897 [GRCh38]
Chr10:97453654 [GRCh37]
Chr10:10q24.1		 pathogenic|likely pathogenic|uncertain significance
NM_015631.6(TCTN3):c.21G>C (p.Ala7=) single nucleotide variant Orofacial-digital syndrome IV [RCV003068261] Chr10:95693879 [GRCh38]
Chr10:97453636 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.201C>T (p.Val67=) single nucleotide variant Orofacial-digital syndrome IV [RCV003057829] Chr10:95693699 [GRCh38]
Chr10:97453456 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.211G>T (p.Val71Leu) single nucleotide variant Orofacial-digital syndrome IV [RCV000650529]|not provided [RCV001697422] Chr10:95693689 [GRCh38]
Chr10:97453446 [GRCh37]
Chr10:10q24.1		 benign|likely benign
NM_015631.6(TCTN3):c.153A>G (p.Ser51=) single nucleotide variant Orofacial-digital syndrome IV [RCV000890434]|not specified [RCV000616961] Chr10:95693747 [GRCh38]
Chr10:97453504 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.181C>A (p.Pro61Thr) single nucleotide variant Inborn genetic diseases [RCV003355572]|Orofacial-digital syndrome IV [RCV001894042] Chr10:95693719 [GRCh38]
Chr10:97453476 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.1A>G (p.Met1Val) single nucleotide variant Joubert syndrome 18 [RCV002468883]|Orofacial-digital syndrome IV [RCV002571430] Chr10:95693899 [GRCh38]
Chr10:97453656 [GRCh37]
Chr10:10q24.1		 pathogenic|likely pathogenic
NM_015631.6(TCTN3):c.9C>A (p.Thr3=) single nucleotide variant Orofacial-digital syndrome IV [RCV000650530] Chr10:95693891 [GRCh38]
Chr10:97453648 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.78C>T (p.Ser26=) single nucleotide variant Orofacial-digital syndrome IV [RCV002633443] Chr10:95693822 [GRCh38]
Chr10:97453579 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.48C>A (p.Phe16Leu) single nucleotide variant Orofacial-digital syndrome IV [RCV002633754] Chr10:95693852 [GRCh38]
Chr10:97453609 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.56G>A (p.Gly19Asp) single nucleotide variant Orofacial-digital syndrome IV [RCV002624904] Chr10:95693844 [GRCh38]
Chr10:97453601 [GRCh37]
Chr10:10q24.1		 uncertain significance
GRCh38/hg38 10q24.1(chr10:95606298-95966000)x1 copy number loss See cases [RCV000053243] Chr10:95606298..95966000 [GRCh38]
Chr10:97366055..97725757 [GRCh37]
Chr10:97356045..97715747 [NCBI36]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.107T>C (p.Leu36Ser) single nucleotide variant Orofacial-digital syndrome IV [RCV002615897] Chr10:95693793 [GRCh38]
Chr10:97453550 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.82C>G (p.Pro28Ala) single nucleotide variant Orofacial-digital syndrome IV [RCV002613234] Chr10:95693818 [GRCh38]
Chr10:97453575 [GRCh37]
Chr10:10q24.1		 uncertain significance
GRCh38/hg38 10q23.33-24.2(chr10:92626680-97755102)x1 copy number loss See cases [RCV000052564] Chr10:92626680..97755102 [GRCh38]
Chr10:94386437..99514859 [GRCh37]
Chr10:94376417..99504849 [NCBI36]
Chr10:10q23.33-24.2		 pathogenic
GRCh38/hg38 10q23.33-24.32(chr10:93181201-101356779)x1 copy number loss See cases [RCV000052565] Chr10:93181201..101356779 [GRCh38]
Chr10:94940958..103116536 [GRCh37]
Chr10:94930948..103106526 [NCBI36]
Chr10:10q23.33-24.32		 pathogenic
NM_015631.6(TCTN3):c.256+11A>G single nucleotide variant Orofacial-digital syndrome IV [RCV003797326] Chr10:95693633 [GRCh38]
Chr10:97453390 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.162T>A (p.Thr54=) single nucleotide variant Orofacial-digital syndrome IV [RCV003806164] Chr10:95693738 [GRCh38]
Chr10:97453495 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.2T>A (p.Met1Lys) single nucleotide variant Orofacial-digital syndrome IV [RCV003806525] Chr10:95693898 [GRCh38]
Chr10:97453655 [GRCh37]
Chr10:10q24.1		 pathogenic
NM_015631.6(TCTN3):c.28C>T (p.Gln10Ter) single nucleotide variant Orofacial-digital syndrome IV [RCV003784362] Chr10:95693872 [GRCh38]
Chr10:97453629 [GRCh37]
Chr10:10q24.1		 pathogenic
NM_015631.6(TCTN3):c.165A>C (p.Ala55=) single nucleotide variant Orofacial-digital syndrome IV [RCV003789297] Chr10:95693735 [GRCh38]
Chr10:97453492 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.198G>A (p.Val66=) single nucleotide variant Orofacial-digital syndrome IV [RCV003799846] Chr10:95693702 [GRCh38]
Chr10:97453459 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.228T>G (p.Pro76=) single nucleotide variant Orofacial-digital syndrome IV [RCV003809864] Chr10:95693672 [GRCh38]
Chr10:97453429 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.132C>T (p.Gly44=) single nucleotide variant Orofacial-digital syndrome IV [RCV003798812] Chr10:95693768 [GRCh38]
Chr10:97453525 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.170G>T (p.Arg57Leu) single nucleotide variant Inborn genetic diseases [RCV004466718] Chr10:95693730 [GRCh38]
Chr10:97453487 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.256+2_256+7del deletion Joubert syndrome and related disorders [RCV003987855]|Orofacial-digital syndrome IV [RCV001379433] Chr10:95693637..95693642 [GRCh38]
Chr10:97453394..97453399 [GRCh37]
Chr10:10q24.1		 likely pathogenic
NM_015631.6(TCTN3):c.114G>T (p.Leu38=) single nucleotide variant Orofacial-digital syndrome IV [RCV002168836] Chr10:95693786 [GRCh38]
Chr10:97453543 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.18C>T (p.Leu6=) single nucleotide variant Orofacial-digital syndrome IV [RCV002201215] Chr10:95693882 [GRCh38]
Chr10:97453639 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.159G>T (p.Ala53=) single nucleotide variant Orofacial-digital syndrome IV [RCV002137150] Chr10:95693741 [GRCh38]
Chr10:97453498 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.51C>G (p.Pro17=) single nucleotide variant Orofacial-digital syndrome IV [RCV002185024] Chr10:95693849 [GRCh38]
Chr10:97453606 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.219C>T (p.Pro73=) single nucleotide variant Orofacial-digital syndrome IV [RCV002885403] Chr10:95693681 [GRCh38]
Chr10:97453438 [GRCh37]
Chr10:10q24.1		 likely benign
NM_015631.6(TCTN3):c.2T>C (p.Met1Thr) single nucleotide variant Orofacial-digital syndrome IV [RCV002889728] Chr10:95693898 [GRCh38]
Chr10:97453655 [GRCh37]
Chr10:10q24.1		 pathogenic
NM_015631.6(TCTN3):c.191C>T (p.Pro64Leu) single nucleotide variant Orofacial-digital syndrome IV [RCV003053658] Chr10:95693709 [GRCh38]
Chr10:97453466 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.92C>A (p.Ala31Glu) single nucleotide variant Orofacial-digital syndrome IV [RCV003035477] Chr10:95693808 [GRCh38]
Chr10:97453565 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.256G>T (p.Val86Phe) single nucleotide variant Orofacial-digital syndrome IV [RCV003044796] Chr10:95693644 [GRCh38]
Chr10:97453401 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.61C>T (p.Arg21Trp) single nucleotide variant Orofacial-digital syndrome IV [RCV003042530] Chr10:95693839 [GRCh38]
Chr10:97453596 [GRCh37]
Chr10:10q24.1		 uncertain significance
NM_015631.6(TCTN3):c.21G>A (p.Ala7=) single nucleotide variant Orofacial-digital syndrome IV [RCV000951528]|not specified [RCV000250621] Chr10:95693879 [GRCh38]
Chr10:97453636 [GRCh37]
Chr10:10q24.1		 benign|likely benign

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC130004408 COSMIC
GTEx LOC130004408 GTEx
Human Proteome Map LOC130004408 Human Proteome Map
NCBI Gene LOC130004408 ENTREZGENE