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Single allele AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 17, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002266766.2

Allele description [Variation Report for Single allele]

Genes:
  • OGFOD1:2-oxoglutarate and iron dependent oxygenase domain containing 1 [Gene - OMIM - HGNC]
  • ARL2BP:ADP ribosylation factor like GTPase 2 binding protein [Gene - OMIM - HGNC]
  • LOC130059040:ATAC-STARR-seq lymphoblastoid active region 10848 [Gene]
  • LOC130059042:ATAC-STARR-seq lymphoblastoid active region 10849 [Gene]
  • LOC130059043:ATAC-STARR-seq lymphoblastoid active region 10850 [Gene]
  • LOC130059046:ATAC-STARR-seq lymphoblastoid active region 10851 [Gene]
  • LOC130059048:ATAC-STARR-seq lymphoblastoid active region 10852 [Gene]
  • LOC130059051:ATAC-STARR-seq lymphoblastoid active region 10853 [Gene]
  • LOC130059052:ATAC-STARR-seq lymphoblastoid active region 10854 [Gene]
  • LOC130059053:ATAC-STARR-seq lymphoblastoid active region 10855 [Gene]
  • LOC130059054:ATAC-STARR-seq lymphoblastoid active region 10856 [Gene]
  • LOC130059055:ATAC-STARR-seq lymphoblastoid active region 10857 [Gene]
  • LOC130059056:ATAC-STARR-seq lymphoblastoid active region 10862 [Gene]
  • LOC130059060:ATAC-STARR-seq lymphoblastoid active region 10863 [Gene]
  • LOC130059061:ATAC-STARR-seq lymphoblastoid active region 10864 [Gene]
  • LOC130059062:ATAC-STARR-seq lymphoblastoid active region 10865 [Gene]
  • LOC130059063:ATAC-STARR-seq lymphoblastoid active region 10866 [Gene]
  • LOC130059064:ATAC-STARR-seq lymphoblastoid active region 10867 [Gene]
  • LOC130059065:ATAC-STARR-seq lymphoblastoid active region 10869 [Gene]
  • LOC130059066:ATAC-STARR-seq lymphoblastoid active region 10870 [Gene]
  • LOC130059067:ATAC-STARR-seq lymphoblastoid active region 10871 [Gene]
  • LOC130059068:ATAC-STARR-seq lymphoblastoid active region 10872 [Gene]
  • LOC130059069:ATAC-STARR-seq lymphoblastoid active region 10873 [Gene]
  • LOC130059070:ATAC-STARR-seq lymphoblastoid active region 10874 [Gene]
  • LOC130059071:ATAC-STARR-seq lymphoblastoid active region 10875 [Gene]
  • LOC130059072:ATAC-STARR-seq lymphoblastoid active region 10876 [Gene]
  • LOC130059073:ATAC-STARR-seq lymphoblastoid active region 10877 [Gene]
  • LOC130059074:ATAC-STARR-seq lymphoblastoid active region 10878 [Gene]
  • LOC130059075:ATAC-STARR-seq lymphoblastoid active region 10879 [Gene]
  • LOC130059076:ATAC-STARR-seq lymphoblastoid active region 10880 [Gene]
  • LOC130059077:ATAC-STARR-seq lymphoblastoid active region 10881 [Gene]
  • LOC130059082:ATAC-STARR-seq lymphoblastoid active region 10882 [Gene]
  • LOC130059083:ATAC-STARR-seq lymphoblastoid active region 10883 [Gene]
  • LOC130059085:ATAC-STARR-seq lymphoblastoid active region 10884 [Gene]
  • LOC130059087:ATAC-STARR-seq lymphoblastoid active region 10885 [Gene]
  • LOC130059090:ATAC-STARR-seq lymphoblastoid active region 10886 [Gene]
  • LOC130059091:ATAC-STARR-seq lymphoblastoid active region 10887 [Gene]
  • LOC130059093:ATAC-STARR-seq lymphoblastoid active region 10888 [Gene]
  • LOC130059095:ATAC-STARR-seq lymphoblastoid active region 10889 [Gene]
  • LOC130059097:ATAC-STARR-seq lymphoblastoid active region 10890 [Gene]
  • LOC130059098:ATAC-STARR-seq lymphoblastoid active region 10891 [Gene]
  • LOC130059099:ATAC-STARR-seq lymphoblastoid active region 10892 [Gene]
  • LOC130059100:ATAC-STARR-seq lymphoblastoid active region 10894 [Gene]
  • LOC130059101:ATAC-STARR-seq lymphoblastoid active region 10895 [Gene]
  • LOC130059102:ATAC-STARR-seq lymphoblastoid active region 10896 [Gene]
  • LOC130059103:ATAC-STARR-seq lymphoblastoid active region 10897 [Gene]
  • LOC130059105:ATAC-STARR-seq lymphoblastoid active region 10898 [Gene]
  • LOC130059106:ATAC-STARR-seq lymphoblastoid active region 10899 [Gene]
  • LOC130059107:ATAC-STARR-seq lymphoblastoid active region 10900 [Gene]
  • LOC130059109:ATAC-STARR-seq lymphoblastoid active region 10901 [Gene]
  • LOC130059112:ATAC-STARR-seq lymphoblastoid active region 10902 [Gene]
  • LOC130059113:ATAC-STARR-seq lymphoblastoid active region 10903 [Gene]
  • LOC130059114:ATAC-STARR-seq lymphoblastoid active region 10904 [Gene]
  • LOC130059115:ATAC-STARR-seq lymphoblastoid active region 10905 [Gene]
  • LOC130059116:ATAC-STARR-seq lymphoblastoid active region 10906 [Gene]
  • LOC130059036:ATAC-STARR-seq lymphoblastoid silent region 7503 [Gene]
  • LOC130059037:ATAC-STARR-seq lymphoblastoid silent region 7504 [Gene]
  • LOC130059038:ATAC-STARR-seq lymphoblastoid silent region 7505 [Gene]
  • LOC130059039:ATAC-STARR-seq lymphoblastoid silent region 7506 [Gene]
  • LOC130059041:ATAC-STARR-seq lymphoblastoid silent region 7507 [Gene]
  • LOC130059044:ATAC-STARR-seq lymphoblastoid silent region 7508 [Gene]
  • LOC130059045:ATAC-STARR-seq lymphoblastoid silent region 7509 [Gene]
  • LOC130059047:ATAC-STARR-seq lymphoblastoid silent region 7510 [Gene]
  • LOC130059049:ATAC-STARR-seq lymphoblastoid silent region 7511 [Gene]
  • LOC130059050:ATAC-STARR-seq lymphoblastoid silent region 7514 [Gene]
  • LOC130059057:ATAC-STARR-seq lymphoblastoid silent region 7516 [Gene]
  • LOC130059058:ATAC-STARR-seq lymphoblastoid silent region 7517 [Gene]
  • LOC130059059:ATAC-STARR-seq lymphoblastoid silent region 7518 [Gene]
  • LOC130059078:ATAC-STARR-seq lymphoblastoid silent region 7519 [Gene]
  • LOC130059079:ATAC-STARR-seq lymphoblastoid silent region 7520 [Gene]
  • LOC130059080:ATAC-STARR-seq lymphoblastoid silent region 7521 [Gene]
  • LOC130059081:ATAC-STARR-seq lymphoblastoid silent region 7522 [Gene]
  • LOC130059084:ATAC-STARR-seq lymphoblastoid silent region 7523 [Gene]
  • LOC130059086:ATAC-STARR-seq lymphoblastoid silent region 7524 [Gene]
  • LOC130059088:ATAC-STARR-seq lymphoblastoid silent region 7525 [Gene]
  • LOC130059089:ATAC-STARR-seq lymphoblastoid silent region 7526 [Gene]
  • LOC130059092:ATAC-STARR-seq lymphoblastoid silent region 7527 [Gene]
  • LOC130059094:ATAC-STARR-seq lymphoblastoid silent region 7528 [Gene]
  • LOC130059096:ATAC-STARR-seq lymphoblastoid silent region 7529 [Gene]
  • LOC130059104:ATAC-STARR-seq lymphoblastoid silent region 7531 [Gene]
  • LOC130059108:ATAC-STARR-seq lymphoblastoid silent region 7532 [Gene]
  • LOC130059110:ATAC-STARR-seq lymphoblastoid silent region 7533 [Gene]
  • LOC130059111:ATAC-STARR-seq lymphoblastoid silent region 7534 [Gene]
  • LOC126862362:BRD4-independent group 4 enhancer GRCh37_chr16:57095254-57096453 [Gene]
  • BBS2:Bardet-Biedl syndrome 2 [Gene - OMIM - HGNC]
  • CCL17:C-C motif chemokine ligand 17 [Gene - OMIM - HGNC]
  • CCL22:C-C motif chemokine ligand 22 [Gene - OMIM - HGNC]
  • CX3CL1:C-X3-C motif chemokine ligand 1 [Gene - OMIM - HGNC]
  • LOC126862355:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:54965529-54966728 [Gene]
  • LOC126862357:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:55072974-55074173 [Gene]
  • LOC126862359:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:55813055-55814254 [Gene]
  • LOC126862361:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:56946332-56947531 [Gene]
  • FTO:FTO alpha-ketoglutarate dependent dioxygenase [Gene - OMIM - HGNC]
  • FTO-IT1:FTO intronic transcript 1 [Gene - HGNC]
  • GNAO1:G protein subunit alpha o1 [Gene - OMIM - HGNC]
  • GNAO1-AS1:GNAO1 antisense RNA 1 [Gene - HGNC]
  • GNAO1-DT:GNAO1 divergent transcript [Gene - HGNC]
  • LOC126862358:MED14-independent group 3 enhancer GRCh37_chr16:55786457-55787656 [Gene]
  • LOC126862360:MED14-independent group 3 enhancer GRCh37_chr16:56102252-56103451 [Gene]
  • MMP2-AS1:MMP2 antisense RNA 1 [Gene - HGNC]
  • LOC129390796:MPRA-validated peak2606 silencer [Gene]
  • NLRC5:NLR family CARD domain containing 5 [Gene - OMIM - HGNC]
  • NUP93-DT:NUP93 divergent transcript [Gene - HGNC]
  • LOC132090381:Neanderthal introgressed variant-containing enhancer experimental_43479 [Gene]
  • LOC132090382:Neanderthal introgressed variant-containing enhancer experimental_43482 [Gene]
  • LOC132090383:Neanderthal introgressed variant-containing enhancer experimental_43505 [Gene]
  • LOC132090384:Neanderthal introgressed variant-containing enhancer experimental_43539 [Gene]
  • LOC132090385:Neanderthal introgressed variant-containing enhancer experimental_43594 [Gene]
  • LOC132090386:Neanderthal introgressed variant-containing enhancer experimental_43689 [Gene]
  • LOC132090387:Neanderthal introgressed variant-containing enhancer experimental_43712 [Gene]
  • LOC132090388:Neanderthal introgressed variant-containing enhancer experimental_43740 [Gene]
  • LOC126862356:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:54985537-54986736 [Gene]
  • POLR2C:RNA polymerase II subunit C [Gene - OMIM - HGNC]
  • LOC112449716:Sharpr-MPRA regulatory region 10092 [Gene]
  • LOC121587547:Sharpr-MPRA regulatory region 10529 [Gene]
  • LOC125177314:Sharpr-MPRA regulatory region 10961 [Gene]
  • LOC112469005:Sharpr-MPRA regulatory region 12884 [Gene]
  • LOC125177323:Sharpr-MPRA regulatory region 12895 [Gene]
  • LOC121587546:Sharpr-MPRA regulatory region 13851 [Gene]
  • LOC125177320:Sharpr-MPRA regulatory region 1622 [Gene]
  • LOC125177317:Sharpr-MPRA regulatory region 182 [Gene]
  • LOC125177313:Sharpr-MPRA regulatory region 2551 [Gene]
  • LOC112469004:Sharpr-MPRA regulatory region 2679 [Gene]
  • LOC112469006:Sharpr-MPRA regulatory region 3054 [Gene]
  • LOC125177316:Sharpr-MPRA regulatory region 3138 [Gene]
  • LOC125177318:Sharpr-MPRA regulatory region 3823 [Gene]
  • LOC112469003:Sharpr-MPRA regulatory region 5065 [Gene]
  • LOC125177324:Sharpr-MPRA regulatory region 5344 [Gene]
  • LOC125177315:Sharpr-MPRA regulatory region 5485 [Gene]
  • LOC112469007:Sharpr-MPRA regulatory region 5957 [Gene]
  • LOC125177319:Sharpr-MPRA regulatory region 6357 [Gene]
  • LOC125177322:Sharpr-MPRA regulatory region 6435 [Gene]
  • LOC112449717:Sharpr-MPRA regulatory region 7594 [Gene]
  • LOC112469008:Sharpr-MPRA regulatory region 83 [Gene]
  • LOC110120835:VISTA enhancer hs151 [Gene]
  • LOC110120837:VISTA enhancer hs155 [Gene]
  • LOC110120838:VISTA enhancer hs156 [Gene]
  • LOC110120839:VISTA enhancer hs157 [Gene]
  • LOC110120574:VISTA enhancer hs23 [Gene]
  • LOC110120575:VISTA enhancer hs26 [Gene]
  • LOC110120576:VISTA enhancer hs27 [Gene]
  • LOC110120577:VISTA enhancer hs37 [Gene]
  • LOC110120578:VISTA enhancer hs43 [Gene]
  • LOC110120579:VISTA enhancer hs51 [Gene]
  • LOC110120580:VISTA enhancer hs52 [Gene]
  • ADGRG1:adhesion G protein-coupled receptor G1 [Gene - OMIM - HGNC]
  • ADGRG5:adhesion G protein-coupled receptor G5 [Gene - OMIM - HGNC]
  • AMFR:autocrine motility factor receptor [Gene - OMIM - HGNC]
  • CAPNS2:calpain small subunit 2 [Gene - OMIM - HGNC]
  • CES1:carboxylesterase 1 [Gene - OMIM - HGNC]
  • CES5A:carboxylesterase 5A [Gene - OMIM - HGNC]
  • CETP:cholesteryl ester transfer protein [Gene - OMIM - HGNC]
  • COQ9:coenzyme Q9 [Gene - OMIM - HGNC]
  • CCDC102A:coiled-coil domain containing 102A [Gene - HGNC]
  • CRNDE:colorectal neoplasia differentially expressed [Gene - OMIM - HGNC]
  • CPNE2:copine 2 [Gene - OMIM - HGNC]
  • CIAPIN1:cytokine induced apoptosis inhibitor 1 [Gene - OMIM - HGNC]
  • DOK4:docking protein 4 [Gene - OMIM - HGNC]
  • HERPUD1:homocysteine inducible ER protein with ubiquitin like domain 1 [Gene - OMIM - HGNC]
  • IRX3:iroquois homeobox 3 [Gene - OMIM - HGNC]
  • IRX5:iroquois homeobox 5 [Gene - OMIM - HGNC]
  • IRX6:iroquois homeobox 6 [Gene - OMIM - HGNC]
  • LINC02140:long intergenic non-protein coding RNA 2140 [Gene - HGNC]
  • LINC02169:long intergenic non-protein coding RNA 2169 [Gene - HGNC]
  • LPCAT2:lysophosphatidylcholine acyltransferase 2 [Gene - OMIM - HGNC]
  • MMP2:matrix metallopeptidase 2 [Gene - OMIM - HGNC]
  • MT1A:metallothionein 1A [Gene - OMIM - HGNC]
  • MT1B:metallothionein 1B [Gene - OMIM - HGNC]
  • MT1E:metallothionein 1E [Gene - OMIM - HGNC]
  • MT1F:metallothionein 1F [Gene - OMIM - HGNC]
  • MT1G:metallothionein 1G [Gene - OMIM - HGNC]
  • MT1H:metallothionein 1H [Gene - OMIM - HGNC]
  • MT1M:metallothionein 1M [Gene - OMIM - HGNC]
  • MT1X:metallothionein 1X [Gene - OMIM - HGNC]
  • MT2A:metallothionein 2A [Gene - OMIM - HGNC]
  • MT3:metallothionein 3 [Gene - OMIM - HGNC]
  • MT4:metallothionein 4 [Gene - OMIM - HGNC]
  • MIR138-2:microRNA 138-2 [Gene - OMIM - HGNC]
  • MIR3935:microRNA 3935 [Gene - HGNC]
  • MIR6863:microRNA 6863 [Gene - HGNC]
  • NUP93:nucleoporin 93 [Gene - OMIM - HGNC]
  • NUDT21:nudix hydrolase 21 [Gene - OMIM - HGNC]
  • PLLP:plasmolipin [Gene - OMIM - HGNC]
  • PSME3IP1:proteasome activator subunit 3 interacting protein 1 [Gene - OMIM - HGNC]
  • RSPRY1:ring finger and SPRY domain containing 1 [Gene - OMIM - HGNC]
  • SLC12A3:solute carrier family 12 member 3 [Gene - OMIM - HGNC]
  • SLC6A2:solute carrier family 6 member 2 [Gene - OMIM - HGNC]
  • TRL-CAG2-1:tRNA-Leu (anticodon CAG) 2-1 [Gene - HGNC]
  • TRL-CAG2-2:tRNA-Leu (anticodon CAG) 2-2 [Gene - HGNC]
  • LOC101927480:uncharacterized LOC101927480 [Gene]
  • LOC102725116:uncharacterized LOC102725116 [Gene]
Variant type:
Deletion
Cytogenetic location:
16q12.2-21
Genomic location:
Chr16: 53818483 - 57631312 (on Assembly GRCh38)
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002548861New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Pathogenic
(Sep 17, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002548861.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The 3.81MB 16q12.2q21 deletion identified here has not been observed in the Database of Genomic Variants (DVG) nor in gnomAD SVs(v2.1) suggesting it is not a common benign variant in the populations represented in this database. This variant is not reported in ClinVar, and while the exact deletion identified here has not been reported in affected individuals in the literature, deletions with similar genomic content or fully contained within this deletion have been reported in three individuals [PMID: 32045705, 20803649]. The 3.81MB, 16q12.2q21 copy number loss identified here is reported as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Oct 14, 2023