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NM_001005373.4(LRSAM1):c.1225C>G (p.Gln409Glu)

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Interpretation:
Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000365027.7
Variation ID:
365027
Description:
single nucleotide variant
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NM_001005373.4(LRSAM1):c.1225C>G (p.Gln409Glu)

Allele ID
316611
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q33.3
Genomic location
9: 127485801 (GRCh38) GRCh38 UCSC
9: 130248080 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.12:g.127485801C>G
NG_032008.1:g.39316C>G
NM_001005373.4:c.1225C>G MANE Select NP_001005373.1:p.Gln409Glu missense
... more HGVS
Protein change
Q409E, Q146E
Other names
-
Canonical SPDI
NC_000009.12:127485800:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00037
Trans-Omics for Precision Medicine (TOPMed) 0.00044
Exome Aggregation Consortium (ExAC) 0.00045
The Genome Aggregation Database (gnomAD) 0.00039
The Genome Aggregation Database (gnomAD), exomes 0.00043
The Genome Aggregation Database (gnomAD) 0.00038
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00077
Links
ClinGen: CA5246895
dbSNP: rs149540339
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 7, 2020 RCV000476861.9
Likely benign 1 criteria provided, single submitter - RCV001174262.2
Likely benign 1 criteria provided, single submitter Mar 26, 2020 RCV001706606.1

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LRSAM1 - - GRCh38
GRCh37
522 561

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease type 2P
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000477222.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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 … (more)
Likely benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease type 2P
Allele origin: germline
Invitae
Accession: SCV000547855.6
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Mar 26, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000713990.2
Submitted: (Sep 23, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 32376792)
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease
Allele origin: germline
Molecular Genetics Laboratory,London Health Sciences Centre
Accession: SCV001337392.1
Submitted: (Apr 07, 2020)
Evidence details
not provided
(-)
no assertion provided
Method: phenotyping only
Charcot-Marie-Tooth disease type 2P
Allele origin: unknown
GenomeConnect, ClinGen
Accession: SCV000607242.1
Submitted: (Aug 22, 2017)
Evidence details
Comment:
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs149540339...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 04, 2021