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NC_000020.10:g.(?_389402)_(746418_?)del AND not provided

Germline classification:
no classifications from unflagged records (1 submission)
Review status:
no classifications from unflagged records
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:
RCV001877503.7

Allele description [Variation Report for NC_000020.10:g.(?_389402)_(746418_?)del]

NC_000020.10:g.(?_389402)_(746418_?)del

Genes:
  • RBCK1:RANBP2-type and C3HC4-type zinc finger containing 1 [Gene - OMIM - HGNC]
  • 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:
Deletion
Cytogenetic location:
20p13
Genomic location:
Chr20: 389402 - 746418 (on Assembly GRCh37)
Preferred name:
NC_000020.10:g.(?_389402)_(746418_?)del
HGVS:
NC_000020.10:g.(?_389402)_(746418_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
No clinical assertions found. See "Flagged submissions" below.
Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Loss-of-function mutations in TBC1D20 cause cataracts and male infertility in blind sterile mice and Warburg micro syndrome in humans.

Liegel RP, Handley MT, Ronchetti A, Brown S, Langemeyer L, Linford A, Chang B, Morris-Rosendahl DJ, Carpanini S, Posmyk R, Harthill V, Sheridan E, Abdel-Salam GM, Terhal PA, Faravelli F, Accorsi P, Giordano L, Pinelli L, Hartmann B, Ebert AD, Barr FA, Aligianis IA, et al.

Am J Hum Genet. 2013 Dec 5;93(6):1001-14. doi: 10.1016/j.ajhg.2013.10.011. Epub 2013 Nov 14.

PubMed [citation]
PMID:
24239381
PMCID:
PMC3852926

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002140163.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the TBC1D20 gene has been identified. Loss-of-function variants in TBC1D20 are known to be pathogenic (PMID: 24239381). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with TBC1D20-related conditions. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002140163Labcorp Genetics (formerly Invitae), Labcorp
flagged submission
Reason: This record appears to be redundant with a more recent record from the same submitter.
Notes: SCV002140163 appears to be redundant with SCV002243830.

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 6, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Last Updated: Sep 29, 2024