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Gene: LOC129932529 (ATAC-STARR-seq lymphoblastoid silent region 1823) Homo sapiens

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Symbol:

LOC129932529

Name:

ATAC-STARR-seq lymphoblastoid silent region 1823

RGD ID:

329405336

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	220,094,022 - 220,094,351 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	220,267,364 - 220,267,693 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
T2T-CHM13v2.0	1	219,333,296 - 219,333,625 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
LOC129932529	Human	CATARACTS, GROWTH HORMONE DEFICIENCY, SENSORY NEUROPATHY, SENSORINEURAL HEARING LOSS, AND SKELETAL DYSPLASIA		IAGP	RGD:12840669\|RGD:12842806\|RGD:597695194	8554872	ClinVar Annotator: match by term: Cataracts, growth hormone deficiency, sensory neuropathy, sensorineural hearing loss, and more ...	ClinVar	PMID:25741868\|PMID:28492532
LOC129932529	Human	genetic disease		IAGP	RGD:151728401\|RGD:151873040	8554872	ClinVar Annotator: match by term: Inborn genetic diseases	ClinVar	PMID:25741868\|PMID:28492532
LOC129932529	Human	genetic disease		IAGP	RGD:151714518\|RGD:151814771	8554872	ClinVar Annotator: match by term: Inborn genetic diseases	ClinVar	PMID:28492532
LOC129932529	Human	Usher syndrome		IAGP	RGD:13435444	8554872	ClinVar Annotator: match by term: Usher syndrome	ClinVar	PMID:28041643

PMID:35858748

Variants in LOC129932529
24 total Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
NM_018060.4(IARS2):c.116G>A (p.Arg39Lys)	single nucleotide variant	not provided [RCV004790788]	Chr1:220094332 [GRCh38] Chr1:220267674 [GRCh37] Chr1:1q41	uncertain significance
NM_018060.4(IARS2):c.55C>G (p.Arg19Gly)	single nucleotide variant	Inborn genetic diseases [RCV002557590]\|not provided [RCV001906733]	Chr1:220094271 [GRCh38] Chr1:220267613 [GRCh37] Chr1:1q41	uncertain significance
NM_018060.4(IARS2):c.1A>C (p.Met1Leu)	single nucleotide variant	not provided [RCV004590860]	Chr1:220094217 [GRCh38] Chr1:220267559 [GRCh37] Chr1:1q41	pathogenic
NM_018060.4(IARS2):c.68G>A (p.Gly23Glu)	single nucleotide variant	Inborn genetic diseases [RCV002548820]\|not provided [RCV002021043]	Chr1:220094284 [GRCh38] Chr1:220267626 [GRCh37] Chr1:1q41	uncertain significance
NM_018060.4(IARS2):c.16C>T (p.Arg6Cys)	single nucleotide variant	Inborn genetic diseases [RCV004042177]\|not provided [RCV002002665]	Chr1:220094232 [GRCh38] Chr1:220267574 [GRCh37] Chr1:1q41	uncertain significance
GRCh38/hg38 1q32.3-44(chr1:214023812-248918469)x3	copy number gain	See cases [RCV000050981]	Chr1:214023812..248918469 [GRCh38] Chr1:214197155..249212668 [GRCh37] Chr1:212263778..247179291 [NCBI36] Chr1:1q32.3-44	pathogenic
NM_018060.4(IARS2):c.30G>A (p.Pro10=)	single nucleotide variant	not provided [RCV001879637]	Chr1:220094246 [GRCh38] Chr1:220267588 [GRCh37] Chr1:1q41	likely benign\|uncertain significance
GRCh38/hg38 1q41(chr1:215206760-222004068)x1	copy number loss	See cases [RCV000050298]	Chr1:215206760..222004068 [GRCh38] Chr1:215380103..222177410 [GRCh37] Chr1:213446726..220244033 [NCBI36] Chr1:1q41	pathogenic
NM_018060.4(IARS2):c.79C>T (p.Leu27Phe)	single nucleotide variant	Inborn genetic diseases [RCV003164091]\|not provided [RCV001878629]	Chr1:220094295 [GRCh38] Chr1:220267637 [GRCh37] Chr1:1q41	uncertain significance
NM_018060.4(IARS2):c.93G>C (p.Pro31=)	single nucleotide variant	not provided [RCV002182525]	Chr1:220094309 [GRCh38] Chr1:220267651 [GRCh37] Chr1:1q41	likely benign
GRCh38/hg38 1q32.2-44(chr1:209963625-248918469)x3	copy number gain	See cases [RCV000134979]	Chr1:209963625..248918469 [GRCh38] Chr1:210136970..249212668 [GRCh37] Chr1:208203593..247179291 [NCBI36] Chr1:1q32.2-44	pathogenic
GRCh38/hg38 1q41(chr1:215447347-221971832)x3	copy number gain	See cases [RCV000051874]	Chr1:215447347..221971832 [GRCh38] Chr1:215620690..222145174 [GRCh37] Chr1:213687313..220211797 [NCBI36] Chr1:1q41	pathogenic
GRCh38/hg38 1q31.1-42.11(chr1:187143981-224299417)x3	copy number gain	See cases [RCV000051857]	Chr1:187143981..224299417 [GRCh38] Chr1:187113113..224487119 [GRCh37] Chr1:185379736..222553742 [NCBI36] Chr1:1q31.1-42.11	pathogenic
GRCh38/hg38 1q32.2-44(chr1:209646207-248931113)x3	copy number gain	See cases [RCV000051861]	Chr1:209646207..248931113 [GRCh38] Chr1:209819552..249225312 [GRCh37] Chr1:207886175..247191935 [NCBI36] Chr1:1q32.2-44	pathogenic
NM_018060.4(IARS2):c.85T>C (p.Cys29Arg)	single nucleotide variant	not provided [RCV002880552]	Chr1:220094301 [GRCh38] Chr1:220267643 [GRCh37] Chr1:1q41	uncertain significance
NM_018060.3(IARS2):c.-128T>A	single nucleotide variant	not provided [RCV000835887]	Chr1:220094089 [GRCh38] Chr1:220267431 [GRCh37] Chr1:1q41	likely benign
NM_018060.4(IARS2):c.101A>G (p.Gln34Arg)	single nucleotide variant	not provided [RCV002857174]	Chr1:220094317 [GRCh38] Chr1:220267659 [GRCh37] Chr1:1q41	uncertain significance
NM_018060.4(IARS2):c.78C>T (p.Arg26=)	single nucleotide variant	not provided [RCV002161481]	Chr1:220094294 [GRCh38] Chr1:220267636 [GRCh37] Chr1:1q41	likely benign
NM_018060.4(IARS2):c.32G>T (p.Gly11Val)	single nucleotide variant	not provided [RCV003024206]	Chr1:220094248 [GRCh38] Chr1:220267590 [GRCh37] Chr1:1q41	uncertain significance
NM_018060.4(IARS2):c.25G>A (p.Gly9Arg)	single nucleotide variant	not provided [RCV003118651]	Chr1:220094241 [GRCh38] Chr1:220267583 [GRCh37] Chr1:1q41	uncertain significance
GRCh38/hg38 1q32.1-42.12(chr1:204764914-225408698)x3	copy number gain	See cases [RCV000142054]	Chr1:204764914..225408698 [GRCh38] Chr1:204734042..225596400 [GRCh37] Chr1:203000665..223663023 [NCBI36] Chr1:1q32.1-42.12	pathogenic
Single allele	deletion	Usher syndrome [RCV000505151]	Chr1:216066818..222607612 [GRCh38] Chr1:216240159..222780953 [GRCh37] Chr1:1q41	likely pathogenic
GRCh38/hg38 1q41(chr1:215206760-222004068)x1	copy number loss	See cases [RCV000148255]	Chr1:215206760..222004068 [GRCh38] Chr1:215380103..222177410 [GRCh37] Chr1:213446726..220244033 [NCBI36] Chr1:1q41	pathogenic
NM_018060.4(IARS2):c.23G>T (p.Arg8Leu)	single nucleotide variant	not provided [RCV000676401]\|not specified [RCV000429298]	Chr1:220094239 [GRCh38] Chr1:220267581 [GRCh37] Chr1:1q41	benign\|likely benign
NM_018060.4(IARS2):c.-35G>T	single nucleotide variant	not specified [RCV000616150]	Chr1:220094182 [GRCh38] Chr1:220267524 [GRCh37] Chr1:1q41	likely benign
NM_018060.4(IARS2):c.74C>T (p.Pro25Leu)	single nucleotide variant	not provided [RCV002462449]	Chr1:220094290 [GRCh38] Chr1:220267632 [GRCh37] Chr1:1q41	uncertain significance
GRCh38/hg38 1q32.2-42.13(chr1:228006998-228061271)x2	copy number loss	Orofacial cleft 2 [RCV002481175]	Chr1:228006998..228061271 [GRCh38] Chr1:1q32.2-42.13	association
NM_018060.4(IARS2):c.55C>T (p.Arg19Ter)	single nucleotide variant	not provided [RCV000578626]	Chr1:220094271 [GRCh38] Chr1:220267613 [GRCh37] Chr1:1q41	likely pathogenic\|uncertain significance
NM_018060.4(IARS2):c.18C>T (p.Arg6=)	single nucleotide variant	not provided [RCV003852564]	Chr1:220094234 [GRCh38] Chr1:220267576 [GRCh37] Chr1:1q41	likely benign
NM_018060.4(IARS2):c.6T>C (p.Arg2=)	single nucleotide variant	not provided [RCV003871045]	Chr1:220094222 [GRCh38] Chr1:220267564 [GRCh37] Chr1:1q41	likely benign
NM_018060.4(IARS2):c.34G>A (p.Ala12Thr)	single nucleotide variant	Cataract-growth hormone deficiency-sensory neuropathy-sensorineural hearing loss-skeletal dysplasia syndrome [RCV005007754]\|not provided [RCV005112633]	Chr1:220094250 [GRCh38] Chr1:220267592 [GRCh37] Chr1:1q41	uncertain significance
NM_018060.4(IARS2):c.41C>T (p.Ala14Val)	single nucleotide variant	IARS2-related disorder [RCV003970150]\|not provided [RCV000676402]\|not specified [RCV000435089]	Chr1:220094257 [GRCh38] Chr1:220267599 [GRCh37] Chr1:1q41	benign
NM_018060.4(IARS2):c.111G>C (p.Thr37=)	single nucleotide variant	IARS2-related disorder [RCV003922747]\|not provided [RCV000964849]\|not specified [RCV000431155]	Chr1:220094327 [GRCh38] Chr1:220267669 [GRCh37] Chr1:1q41	benign
GRCh38/hg38 1q32.2-44(chr1:207346642-248930485)x3	copy number gain	See cases [RCV000143727]	Chr1:207346642..248930485 [GRCh38] Chr1:207519987..249224684 [GRCh37] Chr1:205586610..247191307 [NCBI36] Chr1:1q32.2-44	pathogenic
NM_018060.4(IARS2):c.33C>T (p.Gly11=)	single nucleotide variant	not provided [RCV003087673]	Chr1:220094249 [GRCh38] Chr1:220267591 [GRCh37] Chr1:1q41	likely benign

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.


RefSeq Transcripts	NG_165556	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC103590	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068277	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Database	Acc Id	Source(s)
COSMIC	LOC129932529	COSMIC
GTEx	LOC129932529	GTEx
Human Proteome Map	LOC129932529	Human Proteome Map
NCBI Gene	LOC129932529	ENTREZGENE

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailable


InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailable


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