In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. This variant has not been reported in the literature in individuals affected with GSN-related conditions. This variant is present in population databases (rs142305374, gnomAD 0.01%). This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 96 of the GSN protein (p.Val96Ile).
ClinVar Genomic variation as it relates to human health
NM_198252.3(GSN):c.133G>A (p.Val45Ile)
Germline
Classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
(2)
Help
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Conflicting classifications of pathogenicity
Uncertain significance(1); Likely benign(1)
Uncertain significance(1); Likely benign(1)
2
criteria provided, conflicting classifications
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_198252.3(GSN):c.133G>A (p.Val45Ile)
Variation ID: 2991007 Accession: VCV002991007.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 9q33.2 9: 121302104 (GRCh38) [ NCBI UCSC ] 9: 124064382 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Feb 29, 2024 May 1, 2024 Dec 21, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_198252.3:c.133G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_937895.1:p.Val45Ile missense NM_000177.4:c.286G>A NM_000177.5:c.286G>A NP_000168.1:p.Val96Ile missense NM_001127662.2:c.133G>A NP_001121134.1:p.Val45Ile missense NM_001127663.2:c.241G>A NP_001121135.2:p.Val81Ile missense NM_001127664.2:c.133G>A NP_001121136.1:p.Val45Ile missense NM_001127665.2:c.133G>A NP_001121137.1:p.Val45Ile missense NM_001127666.2:c.166G>A NP_001121138.1:p.Val56Ile missense NM_001127667.2:c.166G>A NP_001121139.1:p.Val56Ile missense NM_001258029.2:c.184G>A NP_001244958.1:p.Val62Ile missense NM_001258030.2:c.157G>A NP_001244959.1:p.Val53Ile missense NM_001353053.1:c.133G>A NP_001339982.1:p.Val45Ile missense NM_001353054.1:c.133G>A NP_001339983.1:p.Val45Ile missense NM_001353055.2:c.133G>A NP_001339984.1:p.Val45Ile missense NM_001353056.2:c.133G>A NP_001339985.1:p.Val45Ile missense NM_001353057.2:c.133G>A NP_001339986.1:p.Val45Ile missense NM_001353058.2:c.133G>A NP_001339987.1:p.Val45Ile missense NM_001353059.2:c.133G>A NP_001339988.1:p.Val45Ile missense NM_001353060.2:c.133G>A NP_001339989.1:p.Val45Ile missense NM_001353061.2:c.133G>A NP_001339990.1:p.Val45Ile missense NM_001353062.1:c.133G>A NP_001339991.1:p.Val45Ile missense NM_001353063.2:c.166G>A NP_001339992.1:p.Val56Ile missense NM_001353064.2:c.166G>A NP_001339993.1:p.Val56Ile missense NM_001353065.2:c.166G>A NP_001339994.1:p.Val56Ile missense NM_001353066.2:c.166G>A NP_001339995.1:p.Val56Ile missense NM_001353067.2:c.166G>A NP_001339996.1:p.Val56Ile missense NM_001353068.2:c.166G>A NP_001339997.1:p.Val56Ile missense NM_001353069.2:c.166G>A NP_001339998.1:p.Val56Ile missense NM_001353070.2:c.166G>A NP_001339999.1:p.Val56Ile missense NM_001353071.2:c.166G>A NP_001340000.1:p.Val56Ile missense NM_001353072.2:c.166G>A NP_001340001.1:p.Val56Ile missense NM_001353073.2:c.166G>A NP_001340002.1:p.Val56Ile missense NM_001353074.2:c.166G>A NP_001340003.1:p.Val56Ile missense NM_001353075.1:c.166G>A NP_001340004.1:p.Val56Ile missense NM_001353076.2:c.205G>A NP_001340005.1:p.Val69Ile missense NM_001353077.1:c.166G>A NP_001340006.1:p.Val56Ile missense NM_001353078.2:c.-458-807G>A intron variant NC_000009.12:g.121302104G>A NC_000009.11:g.124064382G>A NG_012872.2:g.106023G>A - Protein change
- V56I, V69I, V53I, V81I, V45I, V96I, V62I
- Other names
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- Canonical SPDI
- NC_000009.12:121302103:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
| GSN | - | - |
GRCh38 GRCh37 |
721 | 757 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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May 1, 2023 | RCV003849670.3 | |
| Likely benign (1) |
criteria provided, single submitter
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Dec 21, 2023 | RCV004366970.1 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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|---|---|---|---|---|---|
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Uncertain significance
(May 01, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004651121.1
First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024 |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant … (more)
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. This variant has not been reported in the literature in individuals affected with GSN-related conditions. This variant is present in population databases (rs142305374, gnomAD 0.01%). This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 96 of the GSN protein (p.Val96Ile). (less)
|
|
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Likely benign
(Dec 21, 2023)
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criteria provided, single submitter
Method: clinical testing
|
Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV004881689.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
|
Comment:
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Germline Functional Evidence
| 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. |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. This variant has not been reported in the literature in individuals affected with GSN-related conditions. This variant is present in population databases (rs142305374, gnomAD 0.01%). This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 96 of the GSN protein (p.Val96Ile).
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Sep 30, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.