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NC_000003.11:g.(?_120365818)_(133465047_?)del AND Alkaptonuria

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 5, 2020
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:
RCV002035459.3

Allele description

NC_000003.11:g.(?_120365818)_(133465047_?)del

Genes:
  • HACD2:3-hydroxyacyl-CoA dehydratase 2 [Gene - OMIM - HGNC]
  • HMCES:5-hydroxymethylcytosine binding, ES cell specific [Gene - OMIM - HGNC]
  • ALG1L2:ALG1 chitobiosyldiphosphodolichol beta-mannosyltransferase like 2 [Gene - HGNC]
  • ATP2C1:ATPase secretory pathway Ca2+ transporting 1 [Gene - OMIM - HGNC]
  • CNBP:CCHC-type zinc finger nucleic acid binding protein [Gene - OMIM - HGNC]
  • CD86:CD86 molecule [Gene - OMIM - HGNC]
  • CDV3:CDV3 homolog [Gene - OMIM - HGNC]
  • COPG1:COPI coat complex subunit gamma 1 [Gene - OMIM - HGNC]
  • POLQ:DNA polymerase theta [Gene - OMIM - HGNC]
  • TOPBP1:DNA topoisomerase II binding protein 1 [Gene - OMIM - HGNC]
  • DNAJB8:DnaJ heat shock protein family (Hsp40) member B8 [Gene - OMIM - HGNC]
  • DNAJC13:DnaJ heat shock protein family (Hsp40) member C13 [Gene - OMIM - HGNC]
  • EFCC1:EF-hand and coiled-coil domain containing 1 [Gene - HGNC]
  • EFCAB12:EF-hand calcium binding domain 12 [Gene - HGNC]
  • EAF2:ELL associated factor 2 [Gene - OMIM - HGNC]
  • FBXO40:F-box protein 40 [Gene - OMIM - HGNC]
  • GATA2:GATA binding protein 2 [Gene - OMIM - HGNC]
  • H1-10:H1.10 linker histone [Gene - OMIM - HGNC]
  • H1-8:H1.8 linker histone [Gene - HGNC]
  • HSPBAP1:HSPB1 associated protein 1 [Gene - OMIM - HGNC]
  • IQCB1:IQ motif containing B1 [Gene - OMIM - HGNC]
  • ISY1:ISY1 splicing factor homolog [Gene - OMIM - HGNC]
  • ISY1-RAB43:ISY1-RAB43 readthrough [Gene - HGNC]
  • KLF15:KLF transcription factor 15 [Gene - OMIM - HGNC]
  • NEK11:NIMA related kinase 11 [Gene - OMIM - HGNC]
  • PRR23E:PRR23 family member E [Gene - HGNC]
  • RABL3:RAB, member of RAS oncogene family like 3 [Gene - OMIM - HGNC]
  • RAB43:RAB43, member RAS oncogene family [Gene - HGNC]
  • RAB7A:RAB7A, member RAS oncogene family [Gene - OMIM - HGNC]
  • RUVBL1:RuvB like AAA ATPase 1 [Gene - OMIM - HGNC]
  • SEC22A:SEC22 homolog A, vesicle trafficking protein [Gene - OMIM - HGNC]
  • SEC61A1:SEC61 translocon subunit alpha 1 [Gene - OMIM - HGNC]
  • WDR5B:WD repeat domain 5B [Gene - HGNC]
  • ZXDC:ZXD family zinc finger C [Gene - OMIM - HGNC]
  • ACP3:acid phosphatase 3 [Gene - OMIM - HGNC]
  • ACAD11:acyl-CoA dehydrogenase family member 11 [Gene - OMIM - HGNC]
  • ACAD9:acyl-CoA dehydrogenase family member 9 [Gene - OMIM - HGNC]
  • ADCY5:adenylate cyclase 5 [Gene - OMIM - HGNC]
  • ALDH1L1:aldehyde dehydrogenase 1 family member L1 [Gene - OMIM - HGNC]
  • ABTB1:ankyrin repeat and BTB domain containing 1 [Gene - OMIM - HGNC]
  • ARGFX:arginine-fifty homeobox [Gene - OMIM - HGNC]
  • ASTE1:asteroid homolog 1 [Gene - HGNC]
  • ACKR4:atypical chemokine receptor 4 [Gene - OMIM - HGNC]
  • BFSP2:beaded filament structural protein 2 [Gene - OMIM - HGNC]
  • CASR:calcium sensing receptor [Gene - OMIM - HGNC]
  • CHST13:carbohydrate sulfotransferase 13 [Gene - OMIM - HGNC]
  • C3orf22:chromosome 3 open reading frame 22 [Gene - HGNC]
  • CFAP100:cilia and flagella associated protein 100 [Gene - HGNC]
  • CFAP92:cilia and flagella associated protein 92 (putative) [Gene - HGNC]
  • CCDC14:coiled-coil domain containing 14 [Gene - OMIM - HGNC]
  • CHCHD6:coiled-coil-helix-coiled-coil-helix domain containing 6 [Gene - OMIM - HGNC]
  • COL6A5:collagen type VI alpha 5 chain [Gene - OMIM - HGNC]
  • COL6A6:collagen type VI alpha 6 chain [Gene - OMIM - HGNC]
  • CPNE4:copine 4 [Gene - OMIM - HGNC]
  • CSTA:cystatin A [Gene - OMIM - HGNC]
  • DTX3L:deltex E3 ubiquitin ligase 3L [Gene - OMIM - HGNC]
  • EEFSEC:eukaryotic elongation factor, selenocysteine-tRNA specific [Gene - OMIM - HGNC]
  • FAM162A:family with sequence similarity 162 member A [Gene - OMIM - HGNC]
  • GTF2E1:general transcription factor IIE subunit 1 [Gene - OMIM - HGNC]
  • GP9:glycoprotein IX platelet [Gene - OMIM - HGNC]
  • GOLGB1:golgin B1 [Gene - OMIM - HGNC]
  • HEG1:heart development protein with EGF like domains 1 [Gene - OMIM - HGNC]
  • HCLS1:hematopoietic cell-specific Lyn substrate 1 [Gene - OMIM - HGNC]
  • HGD:homogentisate 1,2-dioxygenase [Gene - OMIM - HGNC]
  • ILDR1:immunoglobulin like domain containing receptor 1 [Gene - OMIM - HGNC]
  • ITGB5:integrin subunit beta 5 [Gene - OMIM - HGNC]
  • IFT122:intraflagellar transport 122 [Gene - OMIM - HGNC]
  • KALRN:kalirin RhoGEF kinase [Gene - OMIM - HGNC]
  • KPNA1:karyopherin subunit alpha 1 [Gene - OMIM - HGNC]
  • KBTBD12:kelch repeat and BTB domain containing 12 [Gene - HGNC]
  • LINC01565:long intergenic non-protein coding RNA 1565 [Gene - OMIM - HGNC]
  • MBD4:methyl-CpG binding domain 4, DNA glycosylase [Gene - OMIM - HGNC]
  • MCM2:minichromosome maintenance complex component 2 [Gene - OMIM - HGNC]
  • MIX23:mitochondrial matrix import factor 23 [Gene - HGNC]
  • MRPL3:mitochondrial ribosomal protein L3 [Gene - OMIM - HGNC]
  • MGLL:monoglyceride lipase [Gene - OMIM - HGNC]
  • MUC13:mucin 13, cell surface associated [Gene - OMIM - HGNC]
  • MYLK:myosin light chain kinase [Gene - OMIM - HGNC]
  • NPHP3:nephrocystin 3 [Gene - OMIM - HGNC]
  • NUDT16:nudix hydrolase 16 [Gene - OMIM - HGNC]
  • OSBPL11:oxysterol binding protein like 11 [Gene - OMIM - HGNC]
  • PIK3R4:phosphoinositide-3-kinase regulatory subunit 4 [Gene - OMIM - HGNC]
  • PLXNA1:plexin A1 [Gene - OMIM - HGNC]
  • PLXND1:plexin D1 [Gene - OMIM - HGNC]
  • PODXL2:podocalyxin like 2 [Gene - OMIM - HGNC]
  • PARP14:poly(ADP-ribose) polymerase family member 14 [Gene - OMIM - HGNC]
  • PARP15:poly(ADP-ribose) polymerase family member 15 [Gene - OMIM - HGNC]
  • PARP9:poly(ADP-ribose) polymerase family member 9 [Gene - OMIM - HGNC]
  • PDIA5:protein disulfide isomerase family A member 5 [Gene - OMIM - HGNC]
  • RHO:rhodopsin [Gene - OMIM - HGNC]
  • ROPN1:rhophilin associated tail protein 1 [Gene - OMIM - HGNC]
  • ROPN1B:rhophilin associated tail protein 1B [Gene - HGNC]
  • RPN1:ribophorin I [Gene - OMIM - HGNC]
  • SEMA5B:semaphorin 5B [Gene - OMIM - HGNC]
  • SLC12A8:solute carrier family 12 member 8 [Gene - OMIM - HGNC]
  • SLC15A2:solute carrier family 15 member 2 [Gene - OMIM - HGNC]
  • SLC41A3:solute carrier family 41 member 3 [Gene - OMIM - HGNC]
  • SLC49A4:solute carrier family 49 member 4 [Gene - OMIM - HGNC]
  • SNX4:sorting nexin 4 [Gene - OMIM - HGNC]
  • STXBP5L:syntaxin binding protein 5L [Gene - OMIM - HGNC]
  • TXNRD3NB:thioredoxin reductase 3 neighbor [Gene - HGNC]
  • TXNRD3:thioredoxin reductase 3 [Gene - OMIM - HGNC]
  • TRH:thyrotropin releasing hormone [Gene - OMIM - HGNC]
  • TF:transferrin [Gene - OMIM - HGNC]
  • TMCC1:transmembrane and coiled-coil domain family 1 [Gene - OMIM - HGNC]
  • TMEM108:transmembrane protein 108 [Gene - OMIM - HGNC]
  • TPRA1:transmembrane protein adipocyte associated 1 [Gene - OMIM - HGNC]
  • UBA5:ubiquitin like modifier activating enzyme 5 [Gene - OMIM - HGNC]
  • UMPS:uridine monophosphate synthetase [Gene - OMIM - HGNC]
  • UROC1:urocanate hydratase 1 [Gene - OMIM - HGNC]
  • ZNF148:zinc finger protein 148 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3q13.33-22.1
Genomic location:
Chr3: 120365818 - 133465047 (on Assembly GRCh37)
Preferred name:
NC_000003.11:g.(?_120365818)_(133465047_?)del
HGVS:
NC_000003.11:g.(?_120365818)_(133465047_?)del

Condition(s)

Name:
Alkaptonuria (AKU)
Synonyms:
Alcaptonuria; Ochronosis, hereditary; Homogentisic acid oxidase deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008753; MedGen: C0002066; Orphanet: 56; OMIM: 203500

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002234133Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 5, 2020) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Natural history of alkaptonuria.

Phornphutkul C, Introne WJ, Perry MB, Bernardini I, Murphey MD, Fitzpatrick DL, Anderson PD, Huizing M, Anikster Y, Gerber LH, Gahl WA.

N Engl J Med. 2002 Dec 26;347(26):2111-21.

PubMed [citation]
PMID:
12501223

Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

Vilboux T, Kayser M, Introne W, Suwannarat P, Bernardini I, Fischer R, O'Brien K, Kleta R, Huizing M, Gahl WA.

Hum Mutat. 2009 Dec;30(12):1611-9. doi: 10.1002/humu.21120.

PubMed [citation]
PMID:
19862842
PMCID:
PMC2830005
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002234133.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change is a complex rearrangement of the HGD gene. It does not change the copy number and likely represents an inversion which encompasses exons 1-8. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HGD are known to be pathogenic (PMID: 12501223, 19862842). This variant has not been reported in the literature in individuals with HGD-related conditions. 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: Mar 26, 2023