LOC129933535 (ATAC-STARR-seq lymphoblastoid silent region 11384) - Rat Genome Database

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Gene: LOC129933535 (ATAC-STARR-seq lymphoblastoid silent region 11384) Homo sapiens
Analyze
Symbol: LOC129933535
Name: ATAC-STARR-seq lymphoblastoid silent region 11384
RGD ID: 329409060
Description: This genomic sequence represents an accessible chromatin region that was validated as a silencer based on its ability to repress 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
GRCh38239,120,201 - 39,120,920 (+)NCBIGRCh38GRCh38hg38GRCh38
T2T-CHM13v2.0239,129,174 - 39,129,893 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:35858748  


Genomics

Variants

.
Variants in LOC129933535
59 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_005633.4(SOS1):c.67C>T (p.Leu23=) single nucleotide variant Cardiovascular phenotype [RCV002369476] Chr2:39120356 [GRCh38]
Chr2:39347497 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.73C>T (p.Pro25Ser) single nucleotide variant Cardiovascular phenotype [RCV002381283]|Fibromatosis, gingival, 1 [RCV002482943]|RASopathy [RCV000521504]|SOS1-related condition [RCV003934876]|not provided [RCV001711220]|not specified [RCV000154848] Chr2:39120350 [GRCh38]
Chr2:39347491 [GRCh37]
Chr2:2p22.1		 benign|likely benign|uncertain significance
NM_005633.4(SOS1):c.39A>G (p.Glu13=) single nucleotide variant Cardiovascular phenotype [RCV002374457]|Noonan syndrome and Noonan-related syndrome [RCV001813445]|RASopathy [RCV000461204]|not provided [RCV000361364] Chr2:39120384 [GRCh38]
Chr2:39347525 [GRCh37]
Chr2:2p22.1		 likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_005633.4(SOS1):c.87+12G>T single nucleotide variant Fibromatosis, gingival, 1 [RCV002467680]|Noonan syndrome 4 [RCV002467681]|RASopathy [RCV002057147]|not specified [RCV000220265] Chr2:39120324 [GRCh38]
Chr2:39347465 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.-9G>A single nucleotide variant not specified [RCV000128192] Chr2:39120431 [GRCh38]
Chr2:39347572 [GRCh37]
Chr2:2p22.1		 benign
NM_005633.4(SOS1):c.-47C>G single nucleotide variant not specified [RCV000128191] Chr2:39120469 [GRCh38]
Chr2:39347610 [GRCh37]
Chr2:2p22.1		 benign
NM_005633.4(SOS1):c.87+6G>C single nucleotide variant RASopathy [RCV002023716] Chr2:39120330 [GRCh38]
Chr2:39347471 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.51C>T (p.Pro17=) single nucleotide variant RASopathy [RCV001949303] Chr2:39120372 [GRCh38]
Chr2:39347513 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.40G>T (p.Glu14Ter) single nucleotide variant not provided [RCV002267519] Chr2:39120383 [GRCh38]
Chr2:39347524 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.21C>T (p.Pro7=) single nucleotide variant Fibromatosis, gingival, 1 [RCV002467612]|Noonan syndrome 4 [RCV002467613]|RASopathy [RCV002056117]|not provided [RCV003416012]|not specified [RCV000156191] Chr2:39120402 [GRCh38]
Chr2:39347543 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.66A>G (p.Leu22=) single nucleotide variant Cardiovascular phenotype [RCV002363604]|Fibromatosis, gingival, 1 [RCV002468400]|Noonan syndrome 4 [RCV002468401]|RASopathy [RCV002115257] Chr2:39120357 [GRCh38]
Chr2:39347498 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.87+18C>T single nucleotide variant RASopathy [RCV002085625] Chr2:39120318 [GRCh38]
Chr2:39347459 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.40G>A (p.Glu14Lys) single nucleotide variant Cardiovascular phenotype [RCV002323331]|RASopathy [RCV003655364] Chr2:39120383 [GRCh38]
Chr2:39347524 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.28T>G (p.Phe10Val) single nucleotide variant RASopathy [RCV002005559] Chr2:39120395 [GRCh38]
Chr2:39347536 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.87+15G>C single nucleotide variant Fibromatosis, gingival, 1 [RCV002468286]|Noonan syndrome 4 [RCV002468287]|RASopathy [RCV002073325]|not provided [RCV001714937] Chr2:39120321 [GRCh38]
Chr2:39347462 [GRCh37]
Chr2:2p22.1		 benign|likely benign
NM_005633.4(SOS1):c.7G>T (p.Ala3Ser) single nucleotide variant Cardiovascular phenotype [RCV002423053]|Fibromatosis, gingival, 1 [RCV002491910]|RASopathy [RCV001913952]|not provided [RCV003136306] Chr2:39120416 [GRCh38]
Chr2:39347557 [GRCh37]
Chr2:2p22.1		 likely benign|uncertain significance
NM_005633.4(SOS1):c.4C>A (p.Gln2Lys) single nucleotide variant Noonan syndrome [RCV002254876]|RASopathy [RCV003539415] Chr2:39120419 [GRCh38]
Chr2:39347560 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.23A>G (p.Tyr8Cys) single nucleotide variant RASopathy [RCV001898444] Chr2:39120400 [GRCh38]
Chr2:39347541 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.75T>A (p.Pro25=) single nucleotide variant Cardiovascular phenotype [RCV004046614]|RASopathy [RCV002153515] Chr2:39120348 [GRCh38]
Chr2:39347489 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.37G>C (p.Glu13Gln) single nucleotide variant RASopathy [RCV002731327] Chr2:39120386 [GRCh38]
Chr2:39347527 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.38A>G (p.Glu13Gly) single nucleotide variant Fibromatosis, gingival, 1 [RCV002468265]|Noonan syndrome 4 [RCV002468266]|Noonan syndrome [RCV001543121]|RASopathy [RCV002032544]|not provided [RCV003332345] Chr2:39120385 [GRCh38]
Chr2:39347526 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.5A>T (p.Gln2Leu) single nucleotide variant Cardiovascular phenotype [RCV002356466]|Fibromatosis, gingival, 1 [RCV000389511]|Noonan syndrome 4 [RCV000330632] Chr2:39120418 [GRCh38]
Chr2:39347559 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.87+9C>T single nucleotide variant Fibromatosis, gingival, 1 [RCV002467557]|Noonan syndrome 4 [RCV002467558]|Noonan syndrome and Noonan-related syndrome [RCV001813361]|RASopathy [RCV000869195]|SOS1-related condition [RCV003964859]|not specified [RCV000038574] Chr2:39120327 [GRCh38]
Chr2:39347468 [GRCh37]
Chr2:2p22.1		 benign|likely benign
NM_005633.4(SOS1):c.36C>T (p.Ser12=) single nucleotide variant RASopathy [RCV002721951] Chr2:39120387 [GRCh38]
Chr2:39347528 [GRCh37]
Chr2:2p22.1		 likely benign
GRCh38/hg38 2p22.1(chr2:39037204-39369028)x3 copy number gain See cases [RCV000136052] Chr2:39037204..39369028 [GRCh38]
Chr2:39264345..39596169 [GRCh37]
Chr2:39117849..39449673 [NCBI36]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.9G>A (p.Ala3=) single nucleotide variant Cardiovascular phenotype [RCV002382278]|Fibromatosis, gingival, 1 [RCV002468391]|Noonan syndrome 4 [RCV002468392]|RASopathy [RCV002174884] Chr2:39120414 [GRCh38]
Chr2:39347555 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.72G>T (p.Val24=) single nucleotide variant Cardiovascular phenotype [RCV002382783] Chr2:39120351 [GRCh38]
Chr2:39347492 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.23A>T (p.Tyr8Phe) single nucleotide variant Fibromatosis, gingival, 1 [RCV002468232]|Fibromatosis, gingival, 1 [RCV002493725]|Noonan syndrome 4 [RCV001331442]|RASopathy [RCV001863242] Chr2:39120400 [GRCh38]
Chr2:39347541 [GRCh37]
Chr2:2p22.1		 uncertain significance
GRCh38/hg38 2p22.1(chr2:39054693-39369157)x3 copy number gain See cases [RCV000136145] Chr2:39054693..39369157 [GRCh38]
Chr2:39281834..39596298 [GRCh37]
Chr2:39135338..39449802 [NCBI36]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.-1C>T single nucleotide variant Cardiovascular phenotype [RCV002417137] Chr2:39120423 [GRCh38]
Chr2:39347564 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.20C>T (p.Pro7Leu) single nucleotide variant RASopathy [RCV002972559] Chr2:39120403 [GRCh38]
Chr2:39347544 [GRCh37]
Chr2:2p22.1		 likely 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_005633.4(SOS1):c.17T>C (p.Leu6Pro) single nucleotide variant Cardiovascular phenotype [RCV003274107]|RASopathy [RCV002971331] Chr2:39120406 [GRCh38]
Chr2:39347547 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.38_46del (p.Glu13_Asn15del) deletion not specified [RCV003317883] Chr2:39120377..39120385 [GRCh38]
Chr2:39347518..39347526 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.87+6G>T single nucleotide variant Fibromatosis, gingival, 1 [RCV002468144]|Fibromatosis, gingival, 1 [RCV002489704]|Noonan syndrome 4 [RCV002468145]|RASopathy [RCV001068523]|not specified [RCV001420899] Chr2:39120330 [GRCh38]
Chr2:39347471 [GRCh37]
Chr2:2p22.1		 uncertain significance
GRCh38/hg38 2p22.1(chr2:39037130-39390808)x3 copy number gain See cases [RCV000140131] Chr2:39037130..39390808 [GRCh38]
Chr2:39264271..39617949 [GRCh37]
Chr2:39117775..39471453 [NCBI36]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.34A>G (p.Ser12Gly) single nucleotide variant RASopathy [RCV003068725]|not specified [RCV003491220] Chr2:39120389 [GRCh38]
Chr2:39347530 [GRCh37]
Chr2:2p22.1		 uncertain significance
NC_000002.11:g.(?_39278265)_(39347583_?)dup duplication RASopathy [RCV000798814] Chr2:39051124..39120442 [GRCh38]
Chr2:39278265..39347583 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.26A>T (p.Glu9Val) single nucleotide variant Cardiovascular phenotype [RCV002437382] Chr2:39120397 [GRCh38]
Chr2:39347538 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.25G>A (p.Glu9Lys) single nucleotide variant Fibromatosis, gingival, 1 [RCV002493123]|not provided [RCV000680743] Chr2:39120398 [GRCh38]
Chr2:39347539 [GRCh37]
Chr2:2p22.1		 uncertain significance
GRCh38/hg38 2p22.1(chr2:39036084-39379226)x3 copy number gain See cases [RCV000052630] Chr2:39036084..39379226 [GRCh38]
Chr2:39263225..39606367 [GRCh37]
Chr2:39116729..39459871 [NCBI36]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.69G>A (p.Leu23=) single nucleotide variant Cardiovascular phenotype [RCV003187826] Chr2:39120354 [GRCh38]
Chr2:39347495 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.70G>C (p.Val24Leu) single nucleotide variant Cardiovascular phenotype [RCV003283414]|RASopathy [RCV003655419] Chr2:39120353 [GRCh38]
Chr2:39347494 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.27G>A (p.Glu9=) single nucleotide variant Cardiovascular phenotype [RCV002441567] Chr2:39120396 [GRCh38]
Chr2:39347537 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.87+88del deletion not provided [RCV000680665] Chr2:39120248 [GRCh38]
Chr2:39347389 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.21C>G (p.Pro7=) single nucleotide variant RASopathy [RCV000654958]|SOS1-related condition [RCV003892499] Chr2:39120402 [GRCh38]
Chr2:39347543 [GRCh37]
Chr2:2p22.1		 likely benign|uncertain significance
NM_005633.4(SOS1):c.-43C>T single nucleotide variant not specified [RCV000614081] Chr2:39120465 [GRCh38]
Chr2:39347606 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.61G>A (p.Gly21Arg) single nucleotide variant RASopathy [RCV001347175] Chr2:39120362 [GRCh38]
Chr2:39347503 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.31T>C (p.Phe11Leu) single nucleotide variant RASopathy [RCV001315924] Chr2:39120392 [GRCh38]
Chr2:39347533 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.-32C>T single nucleotide variant not provided [RCV000424530] Chr2:39120454 [GRCh38]
Chr2:39347595 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.87+10A>G single nucleotide variant RASopathy [RCV002657943] Chr2:39120326 [GRCh38]
Chr2:39347467 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.34A>T (p.Ser12Cys) single nucleotide variant RASopathy [RCV001327635] Chr2:39120389 [GRCh38]
Chr2:39347530 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.-21C>G single nucleotide variant not provided [RCV000418345] Chr2:39120443 [GRCh38]
Chr2:39347584 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.83A>G (p.Lys28Arg) single nucleotide variant not specified [RCV000413861] Chr2:39120340 [GRCh38]
Chr2:39347481 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.87+16G>C single nucleotide variant RASopathy [RCV003654516] Chr2:39120320 [GRCh38]
Chr2:39347461 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.64C>G (p.Leu22Val) single nucleotide variant RASopathy [RCV003655455] Chr2:39120359 [GRCh38]
Chr2:39347500 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.86A>C (p.Lys29Thr) single nucleotide variant RASopathy [RCV003655560] Chr2:39120337 [GRCh38]
Chr2:39347478 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.11A>G (p.Gln4Arg) single nucleotide variant RASopathy [RCV003655833] Chr2:39120412 [GRCh38]
Chr2:39347553 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.87+19C>G single nucleotide variant RASopathy [RCV003654600] Chr2:39120317 [GRCh38]
Chr2:39347458 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.8C>T (p.Ala3Val) single nucleotide variant RASopathy [RCV003654741] Chr2:39120415 [GRCh38]
Chr2:39347556 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.54G>C (p.Lys18Asn) single nucleotide variant RASopathy [RCV003832305] Chr2:39120369 [GRCh38]
Chr2:39347510 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.48G>A (p.Ala16=) single nucleotide variant RASopathy [RCV003540212] Chr2:39120375 [GRCh38]
Chr2:39347516 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.76G>T (p.Ala26Ser) single nucleotide variant Cardiovascular phenotype [RCV004369199]|RASopathy [RCV003540053] Chr2:39120347 [GRCh38]
Chr2:39347488 [GRCh37]
Chr2:2p22.1		 uncertain significance
NM_005633.4(SOS1):c.-15C>T single nucleotide variant not specified [RCV000151931] Chr2:39120437 [GRCh38]
Chr2:39347578 [GRCh37]
Chr2:2p22.1		 uncertain significance
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
NM_005633.4(SOS1):c.87+16G>T single nucleotide variant RASopathy [RCV003100241] Chr2:39120320 [GRCh38]
Chr2:39347461 [GRCh37]
Chr2:2p22.1		 likely benign
NM_005633.4(SOS1):c.33C>G (p.Phe11Leu) single nucleotide variant RASopathy [RCV001058145] Chr2:39120390 [GRCh38]
Chr2:39347531 [GRCh37]
Chr2:2p22.1		 uncertain significance
GRCh38/hg38 2p22.2-21(chr2:37000557-41954686)x1 copy number loss See cases [RCV000139443] Chr2:37000557..41954686 [GRCh38]
Chr2:37227700..42181826 [GRCh37]
Chr2:37081204..42035330 [NCBI36]
Chr2:2p22.2-21		 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
NC_000002.11:g.(?_39294749)_(39347583_?)dup duplication RASopathy [RCV000546468] Chr2:39067608..39120442 [GRCh38]
Chr2:39294749..39347583 [GRCh37]
Chr2:2p22.1		 uncertain significance

Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129933535 COSMIC
GTEx LOC129933535 GTEx
Human Proteome Map LOC129933535 Human Proteome Map
NCBI Gene LOC129933535 ENTREZGENE