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NM_025137.4(SPG11):c.6625C>T (p.Arg2209Cys)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Feb 6, 2020)
Last evaluated:
Dec 13, 2019
Accession:
VCV000466559.4
Variation ID:
466559
Description:
single nucleotide variant
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NM_025137.4(SPG11):c.6625C>T (p.Arg2209Cys)

Allele ID
465035
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q21.1
Genomic location
15: 44567553 (GRCh38) GRCh38 UCSC
15: 44859751 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.44567553G>A
NC_000015.9:g.44859751G>A
NM_025137.4:c.6625C>T MANE Select NP_079413.3:p.Arg2209Cys missense
... more HGVS
Protein change
R2209C, R2096C
Other names
-
Canonical SPDI
NC_000015.10:44567552:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00028
The Genome Aggregation Database (gnomAD), exomes 0.00023
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00031
Trans-Omics for Precision Medicine (TOPMed) 0.00023
The Genome Aggregation Database (gnomAD) 0.00016
Links
dbSNP: rs374057859
ClinGen: CA7534060
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Dec 13, 2019 RCV000544170.4
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000765209.1
Uncertain significance 1 criteria provided, single submitter Feb 14, 2019 RCV000993048.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SPG11 - - GRCh38
GRCh37
1438 1458

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Amyotrophic lateral sclerosis type 5
Spastic paraplegia 11, autosomal recessive
Charcot-Marie-Tooth disease, axonal type 2X
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000896445.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Feb 14, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001145750.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Dec 13, 2019)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia 11, autosomal recessive
Allele origin: germline
Invitae
Accession: SCV000642272.4
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces arginine with cysteine at codon 2209 of the SPG11 protein (p.Arg2209Cys). The arginine residue is highly conserved and there is a … (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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Title Author Journal Year Link
Twenty years of molecular analyses in amyotrophic lateral sclerosis: genetic landscape of Italian patients. Lamp M Neurobiology of aging 2018 PMID: 29525178
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868

Text-mined citations for rs374057859...

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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 Jun 14, 2021