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NM_025137.4(SPG11):c.3425C>G (p.Ser1142Cys)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: May 26, 2021)
Last evaluated:
Sep 9, 2020
Accession:
VCV000406532.7
Variation ID:
406532
Description:
single nucleotide variant
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NM_025137.4(SPG11):c.3425C>G (p.Ser1142Cys)

Allele ID
400608
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q21.1
Genomic location
15: 44608472 (GRCh38) GRCh38 UCSC
15: 44900670 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.44608472G>C
NC_000015.9:g.44900670G>C
NG_008885.1:g.60207C>G
... more HGVS
Protein change
S1142C
Other names
-
Canonical SPDI
NC_000015.10:44608471:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00010
Exome Aggregation Consortium (ExAC) 0.00011
Trans-Omics for Precision Medicine (TOPMed) 0.00006
The Genome Aggregation Database (gnomAD) 0.00010
Links
ClinGen: CA7534986
dbSNP: rs201082396
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Jun 23, 2020 RCV000462305.7
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000765212.1
Uncertain significance 1 criteria provided, single submitter Sep 9, 2020 RCV001260216.1
Uncertain significance 1 criteria provided, single submitter Apr 1, 2019 RCV001508758.1
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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
1470 1490

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 23, 2020)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia 11, autosomal recessive
Allele origin: germline
Invitae
Accession: SCV000545208.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces serine with cysteine at codon 1142 of the SPG11 protein (p.Ser1142Cys). The serine residue is weakly conserved and there is a … (more)
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: SCV000896448.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia 11, autosomal recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001277237.1
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)
Uncertain significance
(Sep 09, 2020)
criteria provided, single submitter
Method: case-control
Amyotrophic lateral sclerosis
Allele origin: unknown
ALS/MND Lab,University of Malta
Accession: SCV001437185.1
Submitted: (Sep 09, 2020)
Comment:
Single heterozygote
Evidence details
Uncertain significance
(Apr 01, 2019)
criteria provided, single submitter
Method: clinical testing
Not provided
Allele origin: germline
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV001715107.1
Submitted: (May 26, 2021)
Evidence details

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
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 rs201082396...

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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 Nov 20, 2021