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GRCh38/hg38 6q21-22.1(chr6:107370141-115827482)x1 AND See cases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 13, 2012
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000138006.5

Allele description [Variation Report for GRCh38/hg38 6q21-22.1(chr6:107370141-115827482)x1]

GRCh38/hg38 6q21-22.1(chr6:107370141-115827482)x1

Genes:
  • AFG1L:AFG1 like ATPase [Gene - OMIM - HGNC]
  • ARMC2-AS1:ARMC2 antisense RNA 1 [Gene - HGNC]
  • LOC129996929:ATAC-STARR-seq lymphoblastoid active region 24906 [Gene]
  • LOC129996932:ATAC-STARR-seq lymphoblastoid active region 24908 [Gene]
  • LOC129996934:ATAC-STARR-seq lymphoblastoid active region 24909 [Gene]
  • LOC129996935:ATAC-STARR-seq lymphoblastoid active region 24910 [Gene]
  • LOC129996939:ATAC-STARR-seq lymphoblastoid active region 24911 [Gene]
  • LOC129996940:ATAC-STARR-seq lymphoblastoid active region 24912 [Gene]
  • LOC129996941:ATAC-STARR-seq lymphoblastoid active region 24913 [Gene]
  • LOC129996943:ATAC-STARR-seq lymphoblastoid active region 24914 [Gene]
  • LOC129996947:ATAC-STARR-seq lymphoblastoid active region 24915 [Gene]
  • LOC129996948:ATAC-STARR-seq lymphoblastoid active region 24916 [Gene]
  • LOC129996950:ATAC-STARR-seq lymphoblastoid active region 24917 [Gene]
  • LOC129996952:ATAC-STARR-seq lymphoblastoid active region 24918 [Gene]
  • LOC129996953:ATAC-STARR-seq lymphoblastoid active region 24919 [Gene]
  • LOC129996954:ATAC-STARR-seq lymphoblastoid active region 24920 [Gene]
  • LOC129996956:ATAC-STARR-seq lymphoblastoid active region 24921 [Gene]
  • LOC129996958:ATAC-STARR-seq lymphoblastoid active region 24923 [Gene]
  • LOC129996959:ATAC-STARR-seq lymphoblastoid active region 24924 [Gene]
  • LOC129996960:ATAC-STARR-seq lymphoblastoid active region 24925 [Gene]
  • LOC129996962:ATAC-STARR-seq lymphoblastoid active region 24926 [Gene]
  • LOC129996963:ATAC-STARR-seq lymphoblastoid active region 24927 [Gene]
  • LOC129996965:ATAC-STARR-seq lymphoblastoid active region 24928 [Gene]
  • LOC129996966:ATAC-STARR-seq lymphoblastoid active region 24929 [Gene]
  • LOC129996967:ATAC-STARR-seq lymphoblastoid active region 24930 [Gene]
  • LOC129996970:ATAC-STARR-seq lymphoblastoid active region 24931 [Gene]
  • LOC129996971:ATAC-STARR-seq lymphoblastoid active region 24932 [Gene]
  • LOC129996972:ATAC-STARR-seq lymphoblastoid active region 24933 [Gene]
  • LOC129996973:ATAC-STARR-seq lymphoblastoid active region 24934 [Gene]
  • LOC129996976:ATAC-STARR-seq lymphoblastoid active region 24935 [Gene]
  • LOC129996977:ATAC-STARR-seq lymphoblastoid active region 24936 [Gene]
  • LOC129996979:ATAC-STARR-seq lymphoblastoid active region 24937 [Gene]
  • LOC129996980:ATAC-STARR-seq lymphoblastoid active region 24938 [Gene]
  • LOC129996981:ATAC-STARR-seq lymphoblastoid active region 24939 [Gene]
  • LOC129996982:ATAC-STARR-seq lymphoblastoid active region 24940 [Gene]
  • LOC129996985:ATAC-STARR-seq lymphoblastoid active region 24941 [Gene]
  • LOC129996986:ATAC-STARR-seq lymphoblastoid active region 24942 [Gene]
  • LOC129996987:ATAC-STARR-seq lymphoblastoid active region 24943 [Gene]
  • LOC129996988:ATAC-STARR-seq lymphoblastoid active region 24944 [Gene]
  • LOC129996994:ATAC-STARR-seq lymphoblastoid active region 24945 [Gene]
  • LOC129996995:ATAC-STARR-seq lymphoblastoid active region 24946 [Gene]
  • LOC129996996:ATAC-STARR-seq lymphoblastoid active region 24947 [Gene]
  • LOC129996997:ATAC-STARR-seq lymphoblastoid active region 24949 [Gene]
  • LOC129996998:ATAC-STARR-seq lymphoblastoid active region 24950 [Gene]
  • LOC129996999:ATAC-STARR-seq lymphoblastoid active region 24951 [Gene]
  • LOC129997000:ATAC-STARR-seq lymphoblastoid active region 24952 [Gene]
  • LOC129997002:ATAC-STARR-seq lymphoblastoid active region 24953 [Gene]
  • LOC129997003:ATAC-STARR-seq lymphoblastoid active region 24954 [Gene]
  • LOC129997004:ATAC-STARR-seq lymphoblastoid active region 24955 [Gene]
  • LOC129997005:ATAC-STARR-seq lymphoblastoid active region 24956 [Gene]
  • LOC129997006:ATAC-STARR-seq lymphoblastoid active region 24957 [Gene]
  • LOC129997008:ATAC-STARR-seq lymphoblastoid active region 24958 [Gene]
  • LOC129997010:ATAC-STARR-seq lymphoblastoid active region 24959 [Gene]
  • LOC129997011:ATAC-STARR-seq lymphoblastoid active region 24961 [Gene]
  • LOC129997013:ATAC-STARR-seq lymphoblastoid active region 24962 [Gene]
  • LOC129997014:ATAC-STARR-seq lymphoblastoid active region 24963 [Gene]
  • LOC129997015:ATAC-STARR-seq lymphoblastoid active region 24964 [Gene]
  • LOC129997016:ATAC-STARR-seq lymphoblastoid active region 24965 [Gene]
  • LOC129997017:ATAC-STARR-seq lymphoblastoid active region 24966 [Gene]
  • LOC129997018:ATAC-STARR-seq lymphoblastoid active region 24967 [Gene]
  • LOC129997019:ATAC-STARR-seq lymphoblastoid active region 24969 [Gene]
  • LOC129997020:ATAC-STARR-seq lymphoblastoid active region 24970 [Gene]
  • LOC129997022:ATAC-STARR-seq lymphoblastoid active region 24971 [Gene]
  • LOC129997023:ATAC-STARR-seq lymphoblastoid active region 24972 [Gene]
  • LOC129997026:ATAC-STARR-seq lymphoblastoid active region 24974 [Gene]
  • LOC129996927:ATAC-STARR-seq lymphoblastoid silent region 17440 [Gene]
  • LOC129996928:ATAC-STARR-seq lymphoblastoid silent region 17441 [Gene]
  • LOC129996930:ATAC-STARR-seq lymphoblastoid silent region 17442 [Gene]
  • LOC129996931:ATAC-STARR-seq lymphoblastoid silent region 17443 [Gene]
  • LOC129996933:ATAC-STARR-seq lymphoblastoid silent region 17446 [Gene]
  • LOC129996936:ATAC-STARR-seq lymphoblastoid silent region 17448 [Gene]
  • LOC129996937:ATAC-STARR-seq lymphoblastoid silent region 17449 [Gene]
  • LOC129996938:ATAC-STARR-seq lymphoblastoid silent region 17450 [Gene]
  • LOC129996942:ATAC-STARR-seq lymphoblastoid silent region 17451 [Gene]
  • LOC129996944:ATAC-STARR-seq lymphoblastoid silent region 17452 [Gene]
  • LOC129996945:ATAC-STARR-seq lymphoblastoid silent region 17453 [Gene]
  • LOC129996946:ATAC-STARR-seq lymphoblastoid silent region 17454 [Gene]
  • LOC129996949:ATAC-STARR-seq lymphoblastoid silent region 17455 [Gene]
  • LOC129996951:ATAC-STARR-seq lymphoblastoid silent region 17456 [Gene]
  • LOC129996955:ATAC-STARR-seq lymphoblastoid silent region 17457 [Gene]
  • LOC129996957:ATAC-STARR-seq lymphoblastoid silent region 17458 [Gene]
  • LOC129996961:ATAC-STARR-seq lymphoblastoid silent region 17460 [Gene]
  • LOC129996964:ATAC-STARR-seq lymphoblastoid silent region 17462 [Gene]
  • LOC129996968:ATAC-STARR-seq lymphoblastoid silent region 17463 [Gene]
  • LOC129996969:ATAC-STARR-seq lymphoblastoid silent region 17464 [Gene]
  • LOC129996974:ATAC-STARR-seq lymphoblastoid silent region 17465 [Gene]
  • LOC129996975:ATAC-STARR-seq lymphoblastoid silent region 17466 [Gene]
  • LOC129996978:ATAC-STARR-seq lymphoblastoid silent region 17467 [Gene]
  • LOC129996983:ATAC-STARR-seq lymphoblastoid silent region 17472 [Gene]
  • LOC129996984:ATAC-STARR-seq lymphoblastoid silent region 17473 [Gene]
  • LOC129996989:ATAC-STARR-seq lymphoblastoid silent region 17475 [Gene]
  • LOC129996990:ATAC-STARR-seq lymphoblastoid silent region 17476 [Gene]
  • LOC129996991:ATAC-STARR-seq lymphoblastoid silent region 17477 [Gene]
  • LOC129996992:ATAC-STARR-seq lymphoblastoid silent region 17478 [Gene]
  • LOC129996993:ATAC-STARR-seq lymphoblastoid silent region 17479 [Gene]
  • LOC129997001:ATAC-STARR-seq lymphoblastoid silent region 17480 [Gene]
  • LOC129997007:ATAC-STARR-seq lymphoblastoid silent region 17481 [Gene]
  • LOC129997009:ATAC-STARR-seq lymphoblastoid silent region 17484 [Gene]
  • LOC129997012:ATAC-STARR-seq lymphoblastoid silent region 17485 [Gene]
  • LOC129997021:ATAC-STARR-seq lymphoblastoid silent region 17486 [Gene]
  • LOC129997024:ATAC-STARR-seq lymphoblastoid silent region 17487 [Gene]
  • LOC129997025:ATAC-STARR-seq lymphoblastoid silent region 17488 [Gene]
  • LOC126859762:BRD4-independent group 4 enhancer GRCh37_chr6:109612245-109613444 [Gene]
  • LOC126859769:BRD4-independent group 4 enhancer GRCh37_chr6:115322458-115323657 [Gene]
  • CD164:CD164 molecule [Gene - OMIM - HGNC]
  • LOC126859758:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:109019778-109020977 [Gene]
  • LOC126859759:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:109126969-109128168 [Gene]
  • LOC126859768:CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:114317472-114318671 [Gene]
  • DDO:D-aspartate oxidase [Gene - OMIM - HGNC]
  • FIG4:FIG4 phosphoinositide 5-phosphatase [Gene - OMIM - HGNC]
  • FYN:FYN proto-oncogene, Src family tyrosine kinase [Gene - OMIM - HGNC]
  • GPR6:G protein-coupled receptor 6 [Gene - OMIM - HGNC]
  • HDAC2-AS2:HDAC2 and HS3ST5 antisense RNA 2 [Gene - HGNC]
  • LAMA4-AS1:LAMA4 antisense RNA 1 [Gene - HGNC]
  • MROCKI:MARCKS cis regulating lncRNA promoter of cytokines and inflammation [Gene - HGNC]
  • LOC126859760:MED14-independent group 3 enhancer GRCh37_chr6:109218189-109219388 [Gene]
  • LOC126859761:MED14-independent group 3 enhancer GRCh37_chr6:109562791-109563990 [Gene]
  • LOC126859763:MED14-independent group 3 enhancer GRCh37_chr6:110203046-110204245 [Gene]
  • LOC126859764:MED14-independent group 3 enhancer GRCh37_chr6:111428108-111429307 [Gene]
  • LOC126859765:MED14-independent group 3 enhancer GRCh37_chr6:111886439-111887638 [Gene]
  • LOC126859766:MED14-independent group 3 enhancer GRCh37_chr6:112462018-112463217 [Gene]
  • LOC126859770:MED14-independent group 3 enhancer GRCh37_chr6:115391597-115392796 [Gene]
  • LOC128559983:MPRA functional variant 6:109625879:G:A red blood cell enhancer [Gene]
  • LOC129389602:MPRA-validated peak6008 silencer [Gene]
  • LOC129389603:MPRA-validated peak6010 silencer [Gene]
  • LOC129389604:MPRA-validated peak6011 silencer [Gene]
  • LOC129389605:MPRA-validated peak6014 silencer [Gene]
  • LOC129389606:MPRA-validated peak6015 silencer [Gene]
  • LOC129389607:MPRA-validated peak6016 silencer [Gene]
  • LOC129389608:MPRA-validated peak6018 silencer [Gene]
  • LOC129389609:MPRA-validated peak6023 silencer [Gene]
  • LOC129389610:MPRA-validated peak6024 silencer [Gene]
  • LOC129389611:MPRA-validated peak6028 silencer [Gene]
  • LOC129389612:MPRA-validated peak6032 silencer [Gene]
  • LOC129389613:MPRA-validated peak6034 silencer [Gene]
  • LOC129389614:MPRA-validated peak6035 silencer [Gene]
  • LOC129389615:MPRA-validated peak6037 silencer [Gene]
  • LOC129389616:MPRA-validated peak6038 silencer [Gene]
  • LOC129389617:MPRA-validated peak6040 silencer [Gene]
  • LOC129389618:MPRA-validated peak6041 silencer [Gene]
  • LOC129389619:MPRA-validated peak6046 silencer [Gene]
  • LOC129389620:MPRA-validated peak6047 silencer [Gene]
  • LOC132089309:Neanderthal introgressed variant-containing enhancer experimental_87657 [Gene]
  • LOC132089310:Neanderthal introgressed variant-containing enhancer experimental_87727 [Gene]
  • LOC132089311:Neanderthal introgressed variant-containing enhancer experimental_87752 [Gene]
  • LOC132089312:Neanderthal introgressed variant-containing enhancer experimental_87934 [Gene]
  • LOC132089313:Neanderthal introgressed variant-containing enhancer experimental_87979 [Gene]
  • OSTM1-AS1:OSTM1 antisense RNA 1 [Gene - HGNC]
  • LOC126859767:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:112524438-112525637 [Gene]
  • REV3L:REV3 like, DNA directed polymerase zeta catalytic subunit [Gene - OMIM - HGNC]
  • SEC63:SEC63 homolog, protein translocation regulator [Gene - OMIM - HGNC]
  • SCML4:Scm polycomb group protein like 4 [Gene - HGNC]
  • LOC123775403:Sharpr-MPRA regulatory region 10405 [Gene]
  • LOC123833525:Sharpr-MPRA regulatory region 11267 [Gene]
  • LOC121740664:Sharpr-MPRA regulatory region 11311 [Gene]
  • LOC123775399:Sharpr-MPRA regulatory region 11560 [Gene]
  • LOC123775398:Sharpr-MPRA regulatory region 11562 [Gene]
  • LOC123833521:Sharpr-MPRA regulatory region 12211 [Gene]
  • LOC123833523:Sharpr-MPRA regulatory region 12906 [Gene]
  • LOC113121304:Sharpr-MPRA regulatory region 13716 [Gene]
  • LOC123775395:Sharpr-MPRA regulatory region 13974 [Gene]
  • LOC113121302:Sharpr-MPRA regulatory region 14072 [Gene]
  • LOC123775400:Sharpr-MPRA regulatory region 15105 [Gene]
  • LOC123775402:Sharpr-MPRA regulatory region 15445 [Gene]
  • LOC123775396:Sharpr-MPRA regulatory region 2315 [Gene]
  • LOC123833527:Sharpr-MPRA regulatory region 3090 [Gene]
  • LOC121740662:Sharpr-MPRA regulatory region 3191 [Gene]
  • LOC123775397:Sharpr-MPRA regulatory region 5034 [Gene]
  • LOC123775401:Sharpr-MPRA regulatory region 5156 [Gene]
  • LOC113121303:Sharpr-MPRA regulatory region 5191 [Gene]
  • LOC123775405:Sharpr-MPRA regulatory region 5639 [Gene]
  • LOC123775404:Sharpr-MPRA regulatory region 678 [Gene]
  • LOC123775394:Sharpr-MPRA regulatory region 6907 [Gene]
  • LOC123833522:Sharpr-MPRA regulatory region 7524 [Gene]
  • LOC123833526:Sharpr-MPRA regulatory region 9060 [Gene]
  • LOC121740663:Sharpr-MPRA regulatory region 9088 [Gene]
  • LOC123833524:Sharpr-MPRA regulatory region 9187 [Gene]
  • TRAF3IP2:TRAF3 interacting protein 2 [Gene - OMIM - HGNC]
  • TRAF3IP2-AS1:TRAF3IP2 antisense RNA 1 [Gene - HGNC]
  • LOC114803478:TRAF3IP2 eExon liver enhancer [Gene]
  • LOC110121046:VISTA enhancer hs1302 [Gene]
  • LOC110121188:VISTA enhancer hs1690 [Gene]
  • WASF1:WASP family member 1 [Gene - OMIM - HGNC]
  • ZBTB24-DT:ZBTB24 divergent transcript [Gene - HGNC]
  • AMD1:adenosylmethionine decarboxylase 1 [Gene - OMIM - HGNC]
  • AK9:adenylate kinase 9 [Gene - OMIM - HGNC]
  • ARMC2:armadillo repeat containing 2 [Gene - OMIM - HGNC]
  • CDC40:cell division cycle 40 [Gene - OMIM - HGNC]
  • CCN6:cellular communication network factor 6 [Gene - OMIM - HGNC]
  • CEP57L1:centrosomal protein 57 like 1 [Gene - HGNC]
  • C6orf183:chromosome 6 open reading frame 183 [Gene - HGNC]
  • CDK19:cyclin dependent kinase 19 [Gene - OMIM - HGNC]
  • PDSS2:decaprenyl diphosphate synthase subunit 2 [Gene - OMIM - HGNC]
  • FAM229B:family with sequence similarity 229 member B [Gene - HGNC]
  • FOXO3:forkhead box O3 [Gene - OMIM - HGNC]
  • GTF3C6:general transcription factor IIIC subunit 6 [Gene - OMIM - HGNC]
  • HS3ST5:heparan sulfate-glucosamine 3-sulfotransferase 5 [Gene - OMIM - HGNC]
  • HDAC2:histone deacetylase 2 [Gene - OMIM - HGNC]
  • LAMA4:laminin subunit alpha 4 [Gene - OMIM - HGNC]
  • LNCPOIR:lncRNA periodontal mesenchymal stem cell osteogenesis related [Gene - HGNC]
  • LINC00222:long intergenic non-protein coding RNA 222 [Gene - HGNC]
  • LINC02518:long intergenic non-protein coding RNA 2518 [Gene - HGNC]
  • LINC02527:long intergenic non-protein coding RNA 2527 [Gene - HGNC]
  • LINC02534:long intergenic non-protein coding RNA 2534 [Gene - HGNC]
  • LINC02541:long intergenic non-protein coding RNA 2541 [Gene - HGNC]
  • LINC02880:long intergenic non-protein coding RNA 2880 [Gene - HGNC]
  • MFSD4B:major facilitator superfamily domain containing 4B [Gene - OMIM - HGNC]
  • METTL24:methyltransferase like 24 [Gene - HGNC]
  • MICAL1:microtubule associated monooxygenase, calponin and LIM domain containing 1 [Gene - OMIM - HGNC]
  • MARCKS:myristoylated alanine rich protein kinase C substrate [Gene - OMIM - HGNC]
  • NR2E1:nuclear receptor subfamily 2 group E member 1 [Gene - OMIM - HGNC]
  • OSTM1:osteoclastogenesis associated transmembrane protein 1 [Gene - OMIM - HGNC]
  • PPIL6:peptidylprolyl isomerase like 6 [Gene - HGNC]
  • RFPL4B:ret finger protein like 4B [Gene - HGNC]
  • RPF2:ribosome production factor 2 homolog [Gene - OMIM - HGNC]
  • SESN1:sestrin 1 [Gene - OMIM - HGNC]
  • SOBP:sine oculis binding protein homolog [Gene - OMIM - HGNC]
  • SNORD166:small nucleolar RNA, C/D box 166 [Gene - HGNC]
  • SNORA40C:small nucleolar RNA, H/ACA box 40C [Gene - HGNC]
  • SLC16A10:solute carrier family 16 member 10 [Gene - OMIM - HGNC]
  • SLC22A16:solute carrier family 22 member 16 [Gene - OMIM - HGNC]
  • SNX3:sorting nexin 3 [Gene - OMIM - HGNC]
  • SMPD2:sphingomyelin phosphodiesterase 2 [Gene - OMIM - HGNC]
  • TUBE1:tubulin epsilon 1 [Gene - OMIM - HGNC]
  • LOC102724646:uncharacterized LOC102724646 [Gene]
  • ZBTB24:zinc finger and BTB domain containing 24 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
6q21-22.1
Genomic location:
Preferred name:
GRCh38/hg38 6q21-22.1(chr6:107370141-115827482)x1
HGVS:
  • NC_000006.12:g.(?_107370141)_(115827482_?)del
  • NC_000006.10:g.(?_107798038)_(116255339_?)del
  • NC_000006.11:g.(?_107691345)_(116148646_?)del
Links:
dbVar: nssv1494888; dbVar: nsv869193
Observations:
1

Condition(s)

Name:
See cases [See the Variation display for details]
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000178265ISCA site 1

See additional submitters

no assertion criteria provided
Pathogenic
(Jan 13, 2012) 		de novoclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, et al.

Am J Hum Genet. 2010 May 14;86(5):749-64. doi: 10.1016/j.ajhg.2010.04.006. Review.

PubMed [citation]
PMID:
20466091
PMCID:
PMC2869000

Details of each submission

From ISCA site 1, SCV000178265.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providedDiscovery1not providednot providednot provided

Last Updated: May 7, 2024