NM_000187.4(HGD):c.186T>A (p.Tyr62Ter) AND Alkaptonuria

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 2, 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:: RCV002310475.2

Allele description [Variation Report for NM_000187.4(HGD):c.186T>A (p.Tyr62Ter)]

NM_000187.4(HGD):c.186T>A (p.Tyr62Ter)

Gene:

HGD:homogentisate 1,2-dioxygenase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q13.33

Genomic location:

Preferred name:

NM_000187.4(HGD):c.186T>A (p.Tyr62Ter)

HGVS:

NC_000003.12:g.120670523A>T
NG_011957.1:g.16959T>A
NM_000187.4:c.186T>AMANE SELECT
NP_000178.2:p.Tyr62Ter
NC_000003.11:g.120389370A>T

Protein change:

Y62*

Molecular consequence:

NM_000187.4:c.186T>A - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002602461	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Jan 2, 2022)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002602461

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))

Likely pathogenic
(Jan 2, 2022)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Myriad Genetics, Inc., SCV002602461.2

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

Description

NM_000187.3(HGD):c.186T>A(Y62*) is expected to be pathogenic in the context of alkaptonuria. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in HGD, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.

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

Last Updated: Dec 24, 2022

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