NC_000021.8:g.(?_43160998)_(47865240_?)dup AND Cataract 9 multiple types

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 7, 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:: RCV001913783.11

Allele description [Variation Report for NC_000021.8:g.(?_43160998)_(47865240_?)dup]

NC_000021.8:g.(?_43160998)_(47865240_?)dup

Genes:

AGPAT3:1-acylglycerol-3-phosphate O-acyltransferase 3 [Gene - OMIM - HGNC]
ABCG1:ATP binding cassette subfamily G member 1 [Gene - OMIM - HGNC]
C2CD2:C2 calcium dependent domain containing 2 [Gene - OMIM - HGNC]
DNMT3L:DNA methyltransferase 3 like [Gene - OMIM - HGNC]
NDUFV3:NADH:ubiquinone oxidoreductase subunit V3 [Gene - OMIM - HGNC]
PKNOX1:PBX/knotted 1 homeobox 1 [Gene - OMIM - HGNC]
PRDM15:PR/SET domain 15 [Gene - OMIM - HGNC]
PTTG1IP:PTTG1 interacting protein [Gene - OMIM - HGNC]
PWP2:PWP2 small subunit processome component [Gene - OMIM - HGNC]
SLX9:SLX9 ribosome biogenesis factor [Gene - HGNC]
U2AF1:U2 small nuclear RNA auxiliary factor 1 [Gene - OMIM - HGNC]
WDR4:WD repeat domain 4 [Gene - OMIM - HGNC]
ADARB1:adenosine deaminase RNA specific B1 [Gene - OMIM - HGNC]
AIRE:autoimmune regulator [Gene - OMIM - HGNC]
C21orf58:chromosome 21 open reading frame 58 [Gene - HGNC]
CFAP410:cilia and flagella associated protein 410 [Gene - OMIM - HGNC]
COL6A1:collagen type VI alpha 1 chain [Gene - OMIM - HGNC]
COL6A2:collagen type VI alpha 2 chain [Gene - OMIM - HGNC]
COL18A1:collagen type XVIII alpha 1 chain [Gene - OMIM - HGNC]
CRYAA:crystallin alpha A [Gene - OMIM - HGNC]
CBS:cystathionine beta-synthase [Gene - OMIM - HGNC]
CSTB:cystatin B [Gene - OMIM - HGNC]
FTCD:formimidoyltransferase cyclodeaminase [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]
ICOSLG:inducible T cell costimulator ligand [Gene - OMIM - HGNC]
ITGB2:integrin subunit beta 2 [Gene - OMIM - HGNC]
KRTAP10-10:keratin associated protein 10-10 [Gene - HGNC]
KRTAP10-11:keratin associated protein 10-11 [Gene - HGNC]
KRTAP10-12:keratin associated protein 10-12 [Gene - HGNC]
KRTAP10-1:keratin associated protein 10-1 [Gene - HGNC]
KRTAP10-2:keratin associated protein 10-2 [Gene - HGNC]
KRTAP10-3:keratin associated protein 10-3 [Gene - HGNC]
KRTAP10-4:keratin associated protein 10-4 [Gene - HGNC]
KRTAP10-5:keratin associated protein 10-5 [Gene - HGNC]
KRTAP10-6:keratin associated protein 10-6 [Gene - HGNC]
KRTAP10-7:keratin associated protein 10-7 [Gene - HGNC]
KRTAP10-8:keratin associated protein 10-8 [Gene - HGNC]
KRTAP10-9:keratin associated protein 10-9 [Gene - HGNC]
KRTAP12-1:keratin associated protein 12-1 [Gene - HGNC]
KRTAP12-2:keratin associated protein 12-2 [Gene - HGNC]
KRTAP12-3:keratin associated protein 12-3 [Gene - HGNC]
KRTAP12-4:keratin associated protein 12-4 [Gene - HGNC]
LSS:lanosterol synthase [Gene - OMIM - HGNC]
LRRC3:leucine rich repeat containing 3 [Gene - OMIM - HGNC]
LINC00163:long intergenic non-protein coding RNA 163 [Gene - OMIM - HGNC]
LINC00315:long intergenic non-protein coding RNA 315 [Gene - HGNC]
LINC00334:long intergenic non-protein coding RNA 334 [Gene - HGNC]
MCM3AP:minichromosome maintenance complex component 3 associated protein [Gene - OMIM - HGNC]
PCNT:pericentrin [Gene - OMIM - HGNC]
PDE9A:phosphodiesterase 9A [Gene - OMIM - HGNC]
PFKL:phosphofructokinase, liver type [Gene - OMIM - HGNC]
PCBP3:poly(rC) binding protein 3 [Gene - OMIM - HGNC]
POFUT2:protein O-fucosyltransferase 2 [Gene - OMIM - HGNC]
PDXK:pyridoxal kinase [Gene - OMIM - HGNC]
RSPH1:radial spoke head component 1 [Gene - OMIM - HGNC]
RIPK4:receptor interacting serine/threonine kinase 4 [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]
SUMO3:small ubiquitin like modifier 3 [Gene - OMIM - HGNC]
SLC19A1:solute carrier family 19 member 1 [Gene - OMIM - HGNC]
SLC37A1:solute carrier family 37 member 1 [Gene - OMIM - HGNC]
SPATC1L:spermatogenesis and centriole associated 1 like [Gene - OMIM - HGNC]
TSPEAR:thrombospondin type laminin G domain and EAR repeats [Gene - OMIM - HGNC]
TRAPPC10:trafficking protein particle complex subunit 10 [Gene - OMIM - HGNC]
TRPM2:transient receptor potential cation channel subfamily M member 2 [Gene - OMIM - HGNC]
TMPRSS3:transmembrane serine protease 3 [Gene - OMIM - HGNC]
TFF1:trefoil factor 1 [Gene - OMIM - HGNC]
TFF2:trefoil factor 2 [Gene - OMIM - HGNC]
TFF3:trefoil factor 3 [Gene - OMIM - HGNC]
UBASH3A:ubiquitin associated and SH3 domain containing A [Gene - OMIM - HGNC]
UBE2G2:ubiquitin conjugating enzyme E2 G2 [Gene - OMIM - HGNC]
UMODL1:uromodulin like 1 [Gene - OMIM - HGNC]
YBEY:ybeY metalloendoribonuclease [Gene - OMIM - HGNC]
ZBTB21:zinc finger and BTB domain containing 21 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

21q22.3

Genomic location:

Chr21: 43160998 - 47865240 (on Assembly GRCh37)

Preferred name:

NC_000021.8:g.(?_43160998)_(47865240_?)dup

HGVS:

NC_000021.8:g.(?_43160998)_(47865240_?)dup

Condition(s)

Name:: Cataract 9 multiple types
Synonyms:: Cataract 9, multiple types, with or without microcornea; Cataract, autosomal recessive congenital 1
Identifiers:: MONDO: MONDO:0011413; MedGen: C1858679; Orphanet: 1377; OMIM: 604219

Recent activity

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Isogenic wild-type Rep 2
Isogenic wild-type Rep 2

biosample
Arene sp. SWA-2009 voucher MCZ:Mala:378576 28S ribosomal RNA gene, partial seque...
Arene sp. SWA-2009 voucher MCZ:Mala:378576 28S ribosomal RNA gene, partial sequence
gi|290750915|gb|FJ977682.1|

Nucleotide
AGENCOURT_19146027 NICHD_XGC_Te2 Xenopus laevis cDNA clone IMAGE:7208802 5', mRN...
AGENCOURT_19146027 NICHD_XGC_Te2 Xenopus laevis cDNA clone IMAGE:7208802 5', mRNA sequence
gi|43397365|gnl|dbEST|21715851|gb|C 34.1|

Nucleotide
CBXT938.b1 NICHD_XGC_trop_25 Xenopus tropicalis cDNA clone IMAGE:8882853 5', mRN...
CBXT938.b1 NICHD_XGC_trop_25 Xenopus tropicalis cDNA clone IMAGE:8882853 5', mRNA sequence
gi|133817115|gnl|dbEST|45246722|gb| 762.1|

Nucleotide
RecName: Full=Endogenous retrovirus group K member 21 Gag polyprotein; AltName: ...
RecName: Full=Endogenous retrovirus group K member 21 Gag polyprotein; AltName: Full=HERV-K_12q14.1 provirus ancestral Gag polyprotein; Short=Gag polyprotein
gi|50400277|sp|P62683.2|GAK21_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002303766	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 7, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002303766

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 7, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002303766.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

A copy number gain of the genomic region encompassing the full coding sequence of the CRYAA 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 CRYAA-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 16, 2024

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