NM_001161586.3(ME3):c.1660G>A (p.Asp554Asn) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 10, 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:: RCV002968688.1

Allele description [Variation Report for NM_001161586.3(ME3):c.1660G>A (p.Asp554Asn)]

NM_001161586.3(ME3):c.1660G>A (p.Asp554Asn)

Gene:

ME3:malic enzyme 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q14.2

Genomic location:

Preferred name:

NM_001161586.3(ME3):c.1660G>A (p.Asp554Asn)

HGVS:

NC_000011.10:g.86441434C>T
NM_001014811.2:c.1660G>A
NM_001161586.3:c.1660G>A
NM_001351934.2:c.1660G>A
NM_001395868.1:c.1653+1387G>A
NM_006680.3:c.1660G>A
NP_001014811.1:p.Asp554Asn
NP_001155058.1:p.Asp554Asn
NP_001338863.1:p.Asp554Asn
NP_006671.2:p.Asp554Asn
NC_000011.9:g.86152476C>T
NM_001161586.1:c.1660G>A
NR_147828.2:n.1958G>A
NR_147829.2:n.2378G>A
NR_147830.2:n.1931G>A
NR_147831.2:n.2288G>A
NR_172888.1:n.1967G>A
NR_172889.1:n.1891G>A

Protein change:

D554N

Molecular consequence:

NM_001395868.1:c.1653+1387G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001014811.2:c.1660G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001161586.3:c.1660G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351934.2:c.1660G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006680.3:c.1660G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_147828.2:n.1958G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_147829.2:n.2378G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_147830.2:n.1931G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_147831.2:n.2288G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_172888.1:n.1967G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_172889.1:n.1891G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003690640	Ambry Genetics	criteria provided, single submitter (Ambry General Variant Classification Scheme_2022)	Uncertain significance (Feb 10, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003690640

Ambry Genetics

criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)

Uncertain significance
(Feb 10, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	1	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV003690640.1

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

Description

The c.1660G>A (p.D554N) alteration is located in exon 15 (coding exon 14) of the ME3 gene. This alteration results from a G to A substitution at nucleotide position 1660, causing the aspartic acid (D) at amino acid position 554 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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

Last Updated: Feb 13, 2023

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