NM_000187.4(HGD):c.1080G>C (p.Gly360=) AND Alkaptonuria

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely benign (1 submission)
Last evaluated:: Oct 27, 2021
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:: RCV002102302.5

Allele description

NM_000187.4(HGD):c.1080G>C (p.Gly360=)

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.1080G>C (p.Gly360=)

HGVS:

NC_000003.12:g.120633255C>G
NG_011957.1:g.54227G>C
NM_000187.4:c.1080G>CMANE SELECT
NP_000178.2:p.Gly360=
NC_000003.11:g.120352102C>G

Links:

dbSNP: rs752713602

NCBI 1000 Genomes Browser:

rs752713602

Molecular consequence:

NM_000187.4:c.1080G>C - synonymous variant - [Sequence Ontology: SO:0001819]

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

Recent activity

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Rhodococcus sp. HLSBA34 16S ribosomal RNA gene, partial sequence
Rhodococcus sp. HLSBA34 16S ribosomal RNA gene, partial sequence
gi|239775460|gb|FJ999587.1|

Nucleotide
Micromonospora sp. HLSBA37 16S ribosomal RNA gene, partial sequence
Micromonospora sp. HLSBA37 16S ribosomal RNA gene, partial sequence
gi|239775459|gb|FJ999586.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002321598	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Oct 27, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002321598

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Oct 27, 2021)

germline

clinical testing

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

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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

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 Invitae, SCV002321598.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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