NM_000187.4(HGD):c.189G>T (p.Arg63Ser) AND Alkaptonuria

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 18, 2017
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:: RCV000503877.5

Allele description [Variation Report for NM_000187.4(HGD):c.189G>T (p.Arg63Ser)]

NM_000187.4(HGD):c.189G>T (p.Arg63Ser)

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.189G>T (p.Arg63Ser)

HGVS:

NC_000003.12:g.120670520C>A
NG_011957.1:g.16962G>T
NM_000187.4:c.189G>TMANE SELECT
NP_000178.2:p.Arg63Ser
NC_000003.11:g.120389367C>A
NM_000187.3:c.189G>T

Protein change:

R63S

Links:

dbSNP: rs1390061303

NCBI 1000 Genomes Browser:

rs1390061303

Molecular consequence:

NM_000187.4:c.189G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000588378	Genomic Research Center, Shahid Beheshti University of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 18, 2017)	inherited	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004101019	Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences	no assertion criteria provided	Pathogenic	germline	research

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000588378

Genomic Research Center, Shahid Beheshti University of Medical Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 18, 2017)

inherited

clinical testing

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

SCV004101019

Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences

no assertion criteria provided

Pathogenic

germline

research

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	1	not provided	not provided	yes	research
Persian	inherited	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000588378.2

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

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

From Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences, SCV004101019.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	yes	research	not provided

Description

The variant was originally described in AKU patient in https://doi.org/10.1016/j.mgene.2018.09.006. It has been submitted to the HGD gene mutation database (http://hgddatabase.cvtisr.sk/, DB-ID: AKU_00244).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		2	not provided	1	not provided

Last Updated: Nov 11, 2023

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