NC_000023.10:g.(?_152014869)_(154563736_?)del AND Anemia, nonspherocytic hemolytic, due to G6PD deficiency

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:: RCV003122393.6

Allele description [Variation Report for NC_000023.10:g.(?_152014869)_(154563736_?)del]

NC_000023.10:g.(?_152014869)_(154563736_?)del

Genes:

ABCD1:ATP binding cassette subfamily D member 1 [Gene - OMIM - HGNC]
ATP6AP1:ATPase H+ transporting accessory protein 1 [Gene - OMIM - HGNC]
ATP2B3:ATPase plasma membrane Ca2+ transporting 3 [Gene - OMIM - HGNC]
BCAP31:B cell receptor associated protein 31 [Gene - OMIM - HGNC]
BRCC3:BRCA1/BRCA2-containing complex subunit 3 [Gene - OMIM - HGNC]
CMC4:C-X9-C motif containing 4 [Gene - OMIM - HGNC]
FAM3A:FAM3 metabolism regulating signaling molecule A [Gene - OMIM - HGNC]
FUNDC2:FUN14 domain containing 2 [Gene - OMIM - HGNC]
GDI1:GDP dissociation inhibitor 1 [Gene - OMIM - HGNC]
GAB3:GRB2 associated binding protein 3 [Gene - OMIM - HGNC]
H2AB1:H2A.B variant histone 1 [Gene - OMIM - HGNC]
HAUS7:HAUS augmin like complex subunit 7 [Gene - OMIM - HGNC]
LAGE3:L antigen family member 3 [Gene - OMIM - HGNC]
L1CAM:L1 cell adhesion molecule [Gene - OMIM - HGNC]
MAGEA1:MAGE family member A1 [Gene - OMIM - HGNC]
MPP1:MAGUK p55 scaffold protein 1 [Gene - OMIM - HGNC]
NAA10:N-alpha-acetyltransferase 10, NatA catalytic subunit [Gene - OMIM - HGNC]
NSDHL:NAD(P) dependent steroid dehydrogenase-like [Gene - OMIM - HGNC]
PDZD4:PDZ domain containing 4 [Gene - OMIM - HGNC]
PNMA3:PNMA family member 3 [Gene - OMIM - HGNC]
PNMA5:PNMA family member 5 [Gene - OMIM - HGNC]
PNMA6A:PNMA family member 6A [Gene - OMIM - HGNC]
PNMA6E:PNMA family member 6E [Gene - HGNC]
RAB39B:RAB39B, member RAS oncogene family [Gene - OMIM - HGNC]
ARHGAP4:Rho GTPase activating protein 4 [Gene - OMIM - HGNC]
SRPK3:SRSF protein kinase 3 [Gene - OMIM - HGNC]
VBP1:VHL binding protein 1 [Gene - OMIM - HGNC]
ZFP92:ZFP92 zinc finger protein [Gene - HGNC]
AVPR2:arginine vasopressin receptor 2 [Gene - OMIM - HGNC]
BGN:biglycan [Gene - OMIM - HGNC]
CTAG1A:cancer/testis antigen 1A [Gene - OMIM - HGNC]
CTAG1B:cancer/testis antigen 1B [Gene - OMIM - HGNC]
CTAG2:cancer/testis antigen 2 [Gene - OMIM - HGNC]
CLIC2:chloride intracellular channel 2 [Gene - OMIM - HGNC]
F8A1:coagulation factor VIII associated 1 [Gene - OMIM - HGNC]
F8:coagulation factor VIII [Gene - OMIM - HGNC]
CCNQ:cyclin Q [Gene - OMIM - HGNC]
DNASE1L1:deoxyribonuclease 1 like 1 [Gene - OMIM - HGNC]
DUSP9:dual specificity phosphatase 9 [Gene - OMIM - HGNC]
DKC1:dyskerin pseudouridine synthase 1 [Gene - OMIM - HGNC]
EMD:emerin [Gene - OMIM - HGNC]
FAM50A:family with sequence similarity 50 member A [Gene - OMIM - HGNC]
FLNA:filamin A [Gene - OMIM - HGNC]
G6PD:glucose-6-phosphate dehydrogenase [Gene - OMIM - HGNC]
HCFC1:host cell factor C1 [Gene - OMIM - HGNC]
IKBKG:inhibitor of nuclear factor kappa B kinase regulatory subunit gamma [Gene - OMIM - HGNC]
IRAK1:interleukin 1 receptor associated kinase 1 [Gene - OMIM - HGNC]
IDH3G:isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [Gene - OMIM - HGNC]
MTCP1:mature T cell proliferation 1 [Gene - OMIM - HGNC]
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
OPN1LW:opsin 1, long wave sensitive [Gene - OMIM - HGNC]
OPN1MW2:opsin 1, medium wave sensitive 2 [Gene - HGNC]
OPN1MW:opsin 1, medium wave sensitive [Gene - OMIM - HGNC]
PLXNA3:plexin A3 [Gene - OMIM - HGNC]
PLXNB3:plexin B3 [Gene - OMIM - HGNC]
PNCK:pregnancy up-regulated nonubiquitous CaM kinase [Gene - OMIM - HGNC]
RENBP:renin binding protein [Gene - OMIM - HGNC]
RPL10:ribosomal protein L10 [Gene - OMIM - HGNC]
SSR4:signal sequence receptor subunit 4 [Gene - OMIM - HGNC]
SMIM9:small integral membrane protein 9 [Gene - HGNC]
SLC10A3:solute carrier family 10 member 3 [Gene - OMIM - HGNC]
SLC6A8:solute carrier family 6 member 8 [Gene - OMIM - HGNC]
TAFAZZIN:tafazzin, phospholipid-lysophospholipid transacylase [Gene - OMIM - HGNC]
TEX28:testis expressed 28 [Gene - OMIM - HGNC]
TREX2:three prime repair exonuclease 2 [Gene - OMIM - HGNC]
TKTL1:transketolase like 1 [Gene - OMIM - HGNC]
TMEM187:transmembrane protein 187 [Gene - OMIM - HGNC]
UBL4A:ubiquitin like 4A [Gene - OMIM - HGNC]
ZNF185:zinc finger protein 185 with LIM domain [Gene - OMIM - HGNC]
ZNF275:zinc finger protein 275 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq28

Genomic location:

ChrX: 152014869 - 154563736 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_152014869)_(154563736_?)del

HGVS:

NC_000023.10:g.(?_152014869)_(154563736_?)del

Condition(s)

Name:: Anemia, nonspherocytic hemolytic, due to G6PD deficiency (CNSHA1)
Synonyms:: Hemolytic anemia due to G6PD deficiency; Favism, susceptibility to; Class I glucose-6-phosphate dehydrogenase deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010480; MedGen: C2720289; Orphanet: 466026; OMIM: 300908

Recent activity

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Mus musculus cDNA, clone:Y2G0134L23, strand:plus, reference:ENSEMBL:Mouse-Transc...
Mus musculus cDNA, clone:Y2G0134L23, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000018470, based on BLAT search
gi|56039527|dbj|AK215350.1|

Nucleotide
Mus musculus BAC clone RP23-154G20 from 7, complete sequence
Mus musculus BAC clone RP23-154G20 from 7, complete sequence
gi|51854786|gb|AC151477.1||gnl|wugs 3-154G20

Nucleotide
Mus musculus visual cortex cDNA, RIKEN full-length enriched library, clone:K5300...
Mus musculus visual cortex cDNA, RIKEN full-length enriched library, clone:K530012C08 product:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide, full insert sequence
gi|74182824|dbj|AK158932.1|

Nucleotide
Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, cl...
Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830027M05 product:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide, full insert sequence
gi|74191393|dbj|AK151294.1|

Nucleotide
14-3-3 protein beta/alpha [Mus musculus]
14-3-3 protein beta/alpha [Mus musculus]
gi|31543974|ref|NP_061223.2|

Protein

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

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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

Glucose-6-phosphate dehydrogenase deficiency.

Cappellini MD, Fiorelli G.

Lancet. 2008 Jan 5;371(9606):64-74. doi: 10.1016/S0140-6736(08)60073-2. Review.

PubMed [citation]

PMID:: 18177777

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, SCV003790979.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the G6PD gene has been identified. Loss-of-function variants in G6PD are known to be pathogenic (PMID: 18177777). 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 G6PD-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003790979	Labcorp Genetics (formerly Invitae), Labcorp	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003790979 appears to be redundant with SCV003793545. (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 27, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 18177777, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003790979

Labcorp Genetics (formerly Invitae), Labcorp

flagged submission

Reason: This record appears to be redundant with a more recent record from the same submitter.

Notes: SCV003790979 appears to be redundant with SCV003793545.

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 27, 2022)

germline

clinical testing

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

Last Updated: Oct 20, 2024

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