NM_001605.3(AARS1):c.2900A>T (p.Lys967Met) AND Charcot-Marie-Tooth disease axonal type 2N

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jan 13, 2018
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000625089.15

Allele description [Variation Report for NM_001605.3(AARS1):c.2900A>T (p.Lys967Met)]

NM_001605.3(AARS1):c.2900A>T (p.Lys967Met)

Gene:

AARS1:alanyl-tRNA synthetase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_001605.3(AARS1):c.2900A>T (p.Lys967Met)

HGVS:

NC_000016.10:g.70252728T>A
NG_023191.1:g.41782A>T
NM_001605.3:c.2900A>TMANE SELECT
NP_001596.2:p.Lys967Met
NP_001596.2:p.Lys967Met
LRG_359t1:c.2900A>T
LRG_359:g.41782A>T
LRG_359p1:p.Lys967Met
NC_000016.9:g.70286631T>A
NM_001605.2:c.2900A>T

Protein change:

K967M

Links:

dbSNP: rs35744709

NCBI 1000 Genomes Browser:

rs35744709

Molecular consequence:

NM_001605.3:c.2900A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Charcot-Marie-Tooth disease axonal type 2N (CMT2N)
Synonyms:: CHARCOT-MARIE-TOOTH DISEASE, AXONAL, AUTOSOMAL DOMINANT, TYPE 2N; CHARCOT-MARIE-TOOTH NEUROPATHY, AXONAL, TYPE 2N; Charcot-Marie-Tooth disease, type 2N; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013212; MedGen: C2750090; Orphanet: 228174; OMIM: 613287

Recent activity

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intersectin-2 isoform X1 [Homo sapiens]
intersectin-2 isoform X1 [Homo sapiens]
gi|2462573795|ref|XP_054198291.1|

Protein
uncharacterized Golgi apparatus membrane protein-like protein CG5021 isoform X4 ...
uncharacterized Golgi apparatus membrane protein-like protein CG5021 isoform X4 [Trichoplusia ni]
gi|1496288045|ref|XP_026734184.1|

Protein
ankyrin repeat and SAM domain-containing protein 3 isoform X4 [Mus musculus]
ankyrin repeat and SAM domain-containing protein 3 isoform X4 [Mus musculus]
gi|568996339|ref|XP_006522674.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000398648	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV000743755	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Oct 9, 2014)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000398648

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Jan 13, 2018)

germline

clinical testing

Citation Link,

SCV000743755

Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

criteria provided, single submitter

(ACGS Guidelines, 2013)

Likely benign
(Oct 9, 2014)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000398648.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000743755.1

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

#	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		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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