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NC_000016.9:g.(?_46694384)_(48258199_?)dup AND Glycogen storage disease IXb

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 12, 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:
RCV003110959.3

Allele description [Variation Report for NC_000016.9:g.(?_46694384)_(48258199_?)dup]

NC_000016.9:g.(?_46694384)_(48258199_?)dup

Genes:
  • ABCC11:ATP binding cassette subfamily C member 11 [Gene - OMIM - HGNC]
  • ABCC12:ATP binding cassette subfamily C member 12 [Gene - OMIM - HGNC]
  • DNAJA2:DnaJ heat shock protein family (Hsp40) member A2 [Gene - OMIM - HGNC]
  • VPS35:VPS35 retromer complex component [Gene - OMIM - HGNC]
  • C16orf87:chromosome 16 open reading frame 87 [Gene - HGNC]
  • GPT2:glutamic--pyruvic transaminase 2 [Gene - OMIM - HGNC]
  • ITFG1:integrin alpha FG-GAP repeat containing 1 [Gene - OMIM - HGNC]
  • MYLK3:myosin light chain kinase 3 [Gene - OMIM - HGNC]
  • NETO2:neuropilin and tolloid like 2 [Gene - OMIM - HGNC]
  • ORC6:origin recognition complex subunit 6 [Gene - OMIM - HGNC]
  • PHKB:phosphorylase kinase regulatory subunit beta [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
16q11.2-12.1
Genomic location:
Chr16: 46694384 - 48258199 (on Assembly GRCh37)
Preferred name:
NC_000016.9:g.(?_46694384)_(48258199_?)dup
HGVS:
NC_000016.9:g.(?_46694384)_(48258199_?)dup

Condition(s)

Name:
Glycogen storage disease IXb (GSD9B)
Synonyms:
GLYCOGENOSIS OF LIVER AND MUSCLE, AUTOSOMAL RECESSIVE; GSD IXb; PHOSPHORYLASE KINASE DEFICIENCY OF LIVER AND MUSCLE, AUTOSOMAL RECESSIVE
Identifiers:
MONDO: MONDO:0009868; MedGen: C0543514; Orphanet: 79240; OMIM: 261750

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003792084Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 12, 2022) 		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, SCV003792084.2

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the PHKB gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with PHKB-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Nov 11, 2023