ClinVar Genomic variation as it relates to human health
NM_001351169.2(NT5C2):c.1528A>C (p.Thr510Pro)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001351169.2(NT5C2):c.1528A>C (p.Thr510Pro)
Variation ID: 864795 Accession: VCV000864795.9
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q24.32 10: 103089830 (GRCh38) [ NCBI UCSC ] 10: 104849587 (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 Apr 15, 2020 May 1, 2024 Jan 18, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001351169.2:c.1528A>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001338098.1:p.Thr510Pro missense NM_017649.5:c.*12650T>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
3 prime UTR NM_001134373.3:c.1528A>C NP_001127845.1:p.Thr510Pro missense NM_001351170.2:c.1552A>C NP_001338099.1:p.Thr518Pro missense NM_001351171.2:c.1552A>C NP_001338100.1:p.Thr518Pro missense NM_001351172.2:c.1552A>C NP_001338101.1:p.Thr518Pro missense NM_001351173.2:c.1552A>C NP_001338102.1:p.Thr518Pro missense NM_001351174.1:c.1441A>C NP_001338103.1:p.Thr481Pro missense NM_001351175.2:c.1435A>C NP_001338104.1:p.Thr479Pro missense NM_001351176.2:c.955A>C NP_001338105.1:p.Thr319Pro missense NM_001351177.2:c.955A>C NP_001338106.1:p.Thr319Pro missense NM_001351178.2:c.955A>C NP_001338107.1:p.Thr319Pro missense NM_001351179.2:c.955A>C NP_001338108.1:p.Thr319Pro missense NM_001351180.2:c.955A>C NP_001338109.1:p.Thr319Pro missense NM_001351181.2:c.955A>C NP_001338110.1:p.Thr319Pro missense NM_001351182.2:c.955A>C NP_001338111.1:p.Thr319Pro missense NM_001351183.2:c.955A>C NP_001338112.1:p.Thr319Pro missense NM_001351184.2:c.955A>C NP_001338113.1:p.Thr319Pro missense NM_001351185.2:c.955A>C NP_001338114.1:p.Thr319Pro missense NM_001351186.2:c.955A>C NP_001338115.1:p.Thr319Pro missense NM_001351187.2:c.955A>C NP_001338116.1:p.Thr319Pro missense NM_001351188.2:c.955A>C NP_001338117.1:p.Thr319Pro missense NM_001351189.2:c.955A>C NP_001338118.1:p.Thr319Pro missense NM_001351190.2:c.955A>C NP_001338119.1:p.Thr319Pro missense NM_001351191.1:c.955A>C NP_001338120.1:p.Thr319Pro missense NM_001351192.1:c.955A>C NP_001338121.1:p.Thr319Pro missense NM_001351193.1:c.955A>C NP_001338122.1:p.Thr319Pro missense NM_001351194.2:c.814A>C NP_001338123.1:p.Thr272Pro missense NM_001351195.2:c.814A>C NP_001338124.1:p.Thr272Pro missense NM_001351196.2:c.814A>C NP_001338125.1:p.Thr272Pro missense NM_001351197.2:c.955A>C NP_001338126.1:p.Thr319Pro missense NM_012229.5:c.1528A>C NP_036361.1:p.Thr510Pro missense NM_199076.3:c.*12650T>G 3 prime UTR NC_000010.11:g.103089830T>G NC_000010.10:g.104849587T>G NG_042272.1:g.108477A>C - Protein change
- T479P, T272P, T481P, T510P, T319P, T518P
- Other names
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- Canonical SPDI
- NC_000010.11:103089829:T:G
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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.
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
- 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 | ||
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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. |
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CNNM2 | - | - |
GRCh38 GRCh37 |
301 | 376 | |
NT5C2 | - | - |
GRCh38 GRCh37 |
203 | 264 |
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
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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. |
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Uncertain significance (1) |
criteria provided, single submitter
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Mar 25, 2019 | RCV001072063.6 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jan 18, 2023 | RCV003160595.2 |
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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Uncertain significance
(Mar 25, 2019)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 45
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV001237406.5
First in ClinVar: Apr 15, 2020 Last updated: Feb 14, 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with NT5C2-related conditions. This variant is present in population databases (rs766540908, ExAC 0.003%). This sequence change replaces threonine with proline at codon 510 of the NT5C2 protein (p.Thr510Pro). The threonine residue is moderately conserved and there is a small physicochemical difference between threonine and proline. (less)
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Uncertain significance
(Jan 18, 2023)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV003871311.2
First in ClinVar: Apr 15, 2023 Last updated: May 01, 2024 |
Comment:
The c.1528A>C (p.T510P) alteration is located in exon 1 (coding exon 1) of the NT5C2 gene. This alteration results from a A to C substitution … (more)
The c.1528A>C (p.T510P) alteration is located in exon 1 (coding exon 1) of the NT5C2 gene. This alteration results from a A to C substitution at nucleotide position 1528, causing the threonine (T) at amino acid position 510 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
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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. |
Citations for germline classification of this variant
HelpThere 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 rs766540908 ...
HelpRecord last updated May 01, 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.