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GRCh38/hg38 20p13(chr20:453176-822262)x1 AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 1, 2022
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:
RCV002283352.1

Allele description [Variation Report for GRCh38/hg38 20p13(chr20:453176-822262)x1]

GRCh38/hg38 20p13(chr20:453176-822262)x1

Genes:
  • LOC130065267:ATAC-STARR-seq lymphoblastoid active region 17440 [Gene]
  • LOC130065269:ATAC-STARR-seq lymphoblastoid active region 17444 [Gene]
  • LOC130065265:ATAC-STARR-seq lymphoblastoid silent region 12577 [Gene]
  • LOC130065266:ATAC-STARR-seq lymphoblastoid silent region 12578 [Gene]
  • LOC130065268:ATAC-STARR-seq lymphoblastoid silent region 12579 [Gene]
  • LOC130065270:ATAC-STARR-seq lymphoblastoid silent region 12580 [Gene]
  • LOC130065271:ATAC-STARR-seq lymphoblastoid silent region 12581 [Gene]
  • LOC130065272:ATAC-STARR-seq lymphoblastoid silent region 12582 [Gene]
  • LOC130065273:ATAC-STARR-seq lymphoblastoid silent region 12583 [Gene]
  • LOC126862948:BRD4-independent group 4 enhancer GRCh37_chr20:596343-597542 [Gene]
  • LOC129391147:MPRA-validated peak4111 silencer [Gene]
  • LOC121852996:Sharpr-MPRA regulatory region 14258 [Gene]
  • LOC125384558:Sharpr-MPRA regulatory region 5118 [Gene]
  • TBC1D20:TBC1 domain family member 20 [Gene - OMIM - HGNC]
  • CSNK2A1:casein kinase 2 alpha 1 [Gene - OMIM - HGNC]
  • SCRT2:scratch family transcriptional repressor 2 [Gene - HGNC]
  • SLC52A3:solute carrier family 52 member 3 [Gene - OMIM - HGNC]
  • SRXN1:sulfiredoxin 1 [Gene - OMIM - HGNC]
  • TCF15:transcription factor 15 [Gene - OMIM - HGNC]
Variant type:
copy number loss
Cytogenetic location:
20p13
Genomic location:
Chr20: 453176 - 822262 (on Assembly GRCh38)
Preferred name:
GRCh38/hg38 20p13(chr20:453176-822262)x1
HGVS:

    Condition(s)

    Name:
    Stereotypic movement disorder
    Synonyms:
    stereotypies; stereotyped movement disorder
    Identifiers:
    MONDO: MONDO:0002265; MedGen: C0038273
    Name:
    Delayed speech and language development
    Identifiers:
    MedGen: C0454644; Human Phenotype Ontology: HP:0000750
    Name:
    Compulsive behaviors
    Synonyms:
    Obsessive-compulsive behavior
    Identifiers:
    MedGen: C0600104; Human Phenotype Ontology: HP:0000722
    Name:
    Intellectual disability, moderate
    Synonyms:
    Moderae intellectual disability
    Identifiers:
    MedGen: C0026351; Human Phenotype Ontology: HP:0002342
    Name:
    Hypotonia
    Synonyms:
    Muscular hypotonia; poor muscle tone
    Identifiers:
    MedGen: C0026827; Human Phenotype Ontology: HP:0001252

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV002571725HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha
    criteria provided, single submitter

    (ACMG/ClinGen CNV Guidelines, 2019)    		Pathogenic
    (Sep 1, 2022)     		paternalresearch

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

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedpaternalyes1not providednot provided1not providedresearch

    Citations

    PubMed

    Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

    Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

    Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

    PubMed [citation]
    PMID:
    31690835
    PMCID:
    PMC7313390

    Details of each submission

    From HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha, SCV002571725.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not provided1not providednot providedresearch PubMed (1)

    Description

    ACMG codes:2A(+1.0)

    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1paternalyes1not providednot provided1not providednot providednot provided

    Last Updated: Oct 14, 2023