This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 442 of the SNX27 protein (p.Val442Ile). This variant is present in population databases (rs149937418, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SNX27-related conditions. ClinVar contains an entry for this variant (Variation ID: 462808). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.
ClinVar Genomic variation as it relates to human health
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- Interpretation:
-
Uncertain significance
- Review status:
- criteria provided, multiple submitters, no conflicts
- Submissions:
- 2
- First in ClinVar:
- Dec 26, 2017
- Most recent Submission:
- Feb 7, 2023
- Last evaluated:
- Jun 13, 2022
- Accession:
- VCV000462808.7
- Variation ID:
- 462808
- Description:
- single nucleotide variant
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NM_001330723.2(SNX27):c.1324G>A (p.Val442Ile)
- Allele ID
- 447216
- Variant type
- single nucleotide variant
- Variant length
- 1 bp
- Cytogenetic location
- 1q21.3
- Genomic location
- 1: 151692519 (GRCh38) GRCh38 UCSC
- 1: 151664995 (GRCh37) GRCh37 UCSC
- HGVS
-
Nucleotide Protein Molecular
consequenceNM_001330723.2:c.1324G>A MANE Select NP_001317652.1:p.Val442Ile missense NM_030918.6:c.1324G>A NP_112180.4:p.Val442Ile missense NC_000001.11:g.151692519G>A NC_000001.10:g.151664995G>A - Protein change
- V442I
- Other names
- -
- Canonical SPDI
- NC_000001.11:151692518:G:A
- 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 0.00002
- Trans-Omics for Precision Medicine (TOPMed) 0.00005
- The Genome Aggregation Database (gnomAD) 0.00006
- Exome Aggregation Consortium (ExAC) 0.00003
- The Genome Aggregation Database (gnomAD) 0.00003
- Links
- ClinGen: CA1093642
- dbSNP: rs149937418
- 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 | Jun 13, 2022 | RCV000558759.7 | |
| Uncertain significance | 1 | criteria provided, single submitter | Apr 21, 2022 | RCV002528348.1 |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Uncertain significance
(Jun 13, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Severe myoclonic epilepsy in infancy
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV000636263.5
First in ClinVar: Dec 26, 2017 Last updated: Feb 07, 2023 |
Comment:
This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 442 of the SNX27 protein (p.Val442Ile). … (more)
This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 442 of the SNX27 protein (p.Val442Ile). This variant is present in population databases (rs149937418, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SNX27-related conditions. ClinVar contains an entry for this variant (Variation ID: 462808). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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. (less)
|
|
|
Uncertain significance
(Apr 21, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV003607915.1
First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023 |
Comment:
The c.1324G>A (p.V442I) alteration is located in exon 9 (coding exon 9) of the SNX27 gene. This alteration results from a G to A substitution … (more)
The c.1324G>A (p.V442I) alteration is located in exon 9 (coding exon 9) of the SNX27 gene. This alteration results from a G to A substitution at nucleotide position 1324, causing the valine (V) at amino acid position 442 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
Number of individuals with the variant: 1
|
Functional evidence
Help| 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
Help| 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 rs149937418...
HelpThese 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 Feb 07, 2023