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NC_000021.8:g.(?_44838120)_(45629566_?)del AND Progressive myoclonic epilepsy

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 23, 2019
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:
RCV001031044.1

Allele description [Variation Report for NC_000021.8:g.(?_44838120)_(45629566_?)del]

NC_000021.8:g.(?_44838120)_(45629566_?)del

Genes:
  • AGPAT3:1-acylglycerol-3-phosphate O-acyltransferase 3 [Gene - OMIM - HGNC]
  • PWP2:PWP2 small subunit processome component [Gene - OMIM - HGNC]
  • CSTB:cystatin B [Gene - OMIM - HGNC]
  • GATD3:glutamine amidotransferase class 1 domain containing 3 [Gene - OMIM - HGNC]
  • HSF2BP:heat shock transcription factor 2 binding protein [Gene - OMIM - HGNC]
  • PDXK:pyridoxal kinase [Gene - OMIM - HGNC]
  • RRP1:ribosomal RNA processing 1 [Gene - OMIM - HGNC]
  • RRP1B:ribosomal RNA processing 1B [Gene - OMIM - HGNC]
  • SIK1:salt inducible kinase 1 [Gene - OMIM - HGNC]
  • TRAPPC10:trafficking protein particle complex subunit 10 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
21q22.3
Genomic location:
Chr21: 44838120 - 45629566 (on Assembly GRCh37)
Preferred name:
NC_000021.8:g.(?_44838120)_(45629566_?)del
HGVS:
NC_000021.8:g.(?_44838120)_(45629566_?)del

Condition(s)

Name:
Progressive myoclonic epilepsy
Synonyms:
Myoclonic Epilepsies, Progressive; Familial progressive myoclonic epilepsy; Progressive myoclonus epilepsy; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0020074; MedGen: C0751778; Orphanet: 308; OMIM: PS254800

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001194350Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(May 23, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001194350.1

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the CSTB gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals with CSTB-related conditions. Loss-of-function variants in CSTB are known to be pathogenic (PMID: 8596935). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Apr 23, 2022