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NC_000012.11:g.(?_122277634)_(124242579_?)del AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 4, 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:
RCV003111519.3

Allele description

NC_000012.11:g.(?_122277634)_(124242579_?)del

Genes:
  • OGFOD2:2-oxoglutarate and iron dependent oxygenase domain containing 2 [Gene - HGNC]
  • HPD:4-hydroxyphenylpyruvate dioxygenase [Gene - OMIM - HGNC]
  • ARL6IP4:ADP ribosylation factor like GTPase 6 interacting protein 4 [Gene - OMIM - HGNC]
  • ABCB9:ATP binding cassette subfamily B member 9 [Gene - OMIM - HGNC]
  • ATP6V0A2:ATPase H+ transporting V0 subunit a2 [Gene - OMIM - HGNC]
  • BCL7A:BAF chromatin remodeling complex subunit BCL7A [Gene - OMIM - HGNC]
  • CLIP1:CAP-Gly domain containing linker protein 1 [Gene - OMIM - HGNC]
  • DDX55:DEAD-box helicase 55 [Gene - OMIM - HGNC]
  • MPHOSPH9:M-phase phosphoprotein 9 [Gene - OMIM - HGNC]
  • MLXIP:MLX interacting protein [Gene - OMIM - HGNC]
  • RILPL1:Rab interacting lysosomal protein like 1 [Gene - OMIM - HGNC]
  • RILPL2:Rab interacting lysosomal protein like 2 [Gene - OMIM - HGNC]
  • B3GNT4:UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4 [Gene - OMIM - HGNC]
  • VPS33A:VPS33A core subunit of CORVET and HOPS complexes [Gene - OMIM - HGNC]
  • VPS37B:VPS37B subunit of ESCRT-I [Gene - OMIM - HGNC]
  • RSRC2:arginine and serine rich coiled-coil 2 [Gene - OMIM - HGNC]
  • CFAP251:cilia and flagella associated protein 251 [Gene - OMIM - HGNC]
  • CCDC62:coiled-coil domain containing 62 [Gene - OMIM - HGNC]
  • CDK2AP1:cyclin dependent kinase 2 associated protein 1 [Gene - OMIM - HGNC]
  • DENR:density regulated re-initiation and release factor [Gene - OMIM - HGNC]
  • DIABLO:diablo IAP-binding mitochondrial protein [Gene - OMIM - HGNC]
  • EIF2B1:eukaryotic translation initiation factor 2B subunit alpha [Gene - OMIM - HGNC]
  • GTF2H3:general transcription factor IIH subunit 3 [Gene - OMIM - HGNC]
  • HIP1R:huntingtin interacting protein 1 related [Gene - OMIM - HGNC]
  • HCAR1:hydroxycarboxylic acid receptor 1 [Gene - OMIM - HGNC]
  • HCAR2:hydroxycarboxylic acid receptor 2 [Gene - OMIM - HGNC]
  • HCAR3:hydroxycarboxylic acid receptor 3 [Gene - OMIM - HGNC]
  • IL31:interleukin 31 [Gene - OMIM - HGNC]
  • KNTC1:kinetochore associated 1 [Gene - OMIM - HGNC]
  • LRRC43:leucine rich repeat containing 43 [Gene - HGNC]
  • KMT5A:lysine methyltransferase 5A [Gene - OMIM - HGNC]
  • MTRFR:mitochondrial translation release factor in rescue [Gene - OMIM - HGNC]
  • PITPNM2:phosphatidylinositol transfer protein membrane associated 2 [Gene - OMIM - HGNC]
  • PSMD9:proteasome 26S subunit, non-ATPase 9 [Gene - OMIM - HGNC]
  • SNRNP35:small nuclear ribonucleoprotein U11/U12 subunit 35 [Gene - OMIM - HGNC]
  • SBNO1:strawberry notch homolog 1 [Gene - OMIM - HGNC]
  • TCTN2:tectonic family member 2 [Gene - OMIM - HGNC]
  • TMED2:transmembrane p24 trafficking protein 2 [Gene - OMIM - HGNC]
  • ZCCHC8:zinc finger CCHC-type containing 8 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
12q24.31
Genomic location:
Chr12: 122277634 - 124242579 (on Assembly GRCh37)
Preferred name:
NC_000012.11:g.(?_122277634)_(124242579_?)del
HGVS:
NC_000012.11:g.(?_122277634)_(124242579_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003791941Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 4, 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV003791941.2

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

Description

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. This variant has not been reported in the literature in individuals affected with VPS33A-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the VPS33A gene has been identified. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in VPS33A cause disease. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

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

Last Updated: Jun 9, 2024