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NM_000187.4(HGD):c.652del AND Alkaptonuria

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
Aug 10, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000169458.16

Allele description [Variation Report for NM_000187.4(HGD):c.652del]

NM_000187.4(HGD):c.652del

Gene:
HGD:homogentisate 1,2-dioxygenase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3q13.33
Genomic location:
Preferred name:
NM_000187.4(HGD):c.652del
HGVS:
  • NC_000003.12:g.120644444del
  • NG_011957.1:g.43041del
  • NM_000187.4:c.652delMANE SELECT
  • NC_000003.11:g.120363288del
  • NC_000003.11:g.120363291del
  • NM_000187.3:c.652delG
Links:
dbSNP: rs786204662
NCBI 1000 Genomes Browser:
rs786204662
Molecular consequence:
  • NM_000187.4:c.652del - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000220883Counsyl
criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))
Likely pathogenic
(Nov 13, 2014)
unknownliterature only

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

Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015),

Citation Link,

SCV002247062Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Aug 10, 2022)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV004046750Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences
no assertion criteria provided
Pathogenicgermlineresearch

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes43not providednot providedyesresearch
not providedunknownunknownnot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Short-term efficacy of hyaluronic acid joint injections in a case of ochronotic arthropathy.

Toussirot É, Aquaron R.

J Clin Rheumatol. 2013 Apr;19(3):152-3. doi: 10.1097/RHU.0b013e318289e7fa. No abstract available.

PubMed [citation]
PMID:
23519186

Ochronotic rheumatism in Algeria: clinical, radiological, biological and molecular studies--a case study of 14 patients in 11 families.

Ladjouze-Rezig A, Rodriguez de Cordoba S, Aquaron R.

Joint Bone Spine. 2006 May;73(3):284-92. Epub 2005 Jul 7.

PubMed [citation]
PMID:
16085442
See all PubMed Citations (6)

Details of each submission

From Counsyl, SCV000220883.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV002247062.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

ClinVar contains an entry for this variant (Variation ID: 189061). For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with clinical features of alkaptonuria (PMID: 16085442). This variant is present in population databases (rs786204662, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Ala218Profs*11) in the HGD gene. 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).

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

From Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences, SCV004046750.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providedyesresearch PubMed (1)

Description

The variant was originally described in PMID:11001939. It has been submitted to the HGD gene mutation database (http://hgddatabase.cvtisr.sk/, DB-ID: AKU_00069).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided4not provided3not provided

Last Updated: Feb 14, 2024