NM_001698.3(AUH):c.860G>C (p.Arg287Thr) AND 3-methylglutaconic aciduria type 1

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 18, 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:: RCV001963400.3

Allele description

NM_001698.3(AUH):c.860G>C (p.Arg287Thr)

Gene:

AUH:AU RNA binding methylglutaconyl-CoA hydratase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q22.31

Genomic location:

Preferred name:

NM_001698.3(AUH):c.860G>C (p.Arg287Thr)

HGVS:

NC_000009.12:g.91217311C>G
NG_008017.1:g.149614G>C
NM_001306190.2:c.773G>C
NM_001351431.2:c.533G>C
NM_001351432.2:c.533G>C
NM_001351433.2:c.533G>C
NM_001698.3:c.860G>CMANE SELECT
NP_001293119.1:p.Arg258Thr
NP_001338360.1:p.Arg178Thr
NP_001338361.1:p.Arg178Thr
NP_001338362.1:p.Arg178Thr
NP_001689.1:p.Arg287Thr
LRG_449:g.149614G>C
NC_000009.11:g.93979593C>G

Protein change:

R178T

Links:

dbSNP: rs1826877739

NCBI 1000 Genomes Browser:

rs1826877739

Molecular consequence:

NM_001306190.2:c.773G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001351431.2:c.533G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001351432.2:c.533G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001351433.2:c.533G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001698.3:c.860G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: 3-methylglutaconic aciduria type 1
Synonyms:: 3 methylglutaconic aciduria type I; MGA type I; 3 alpha methylglutaconic aciduria type I; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009610; MedGen: C0342727; Orphanet: 67046; OMIM: 250950

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002241506	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 18, 2022)	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

SCV002241506

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 18, 2022)

germline

clinical testing

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

Help

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, SCV002241506.3

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

Description

This sequence change replaces arginine, which is basic and polar, with threonine, which is neutral and polar, at codon 287 of the AUH protein (p.Arg287Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with AUH-related conditions. ClinVar contains an entry for this variant (Variation ID: 1460740). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive.

#	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 20, 2024

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