The c.317T>C (p.M106T) alteration is located in exon 4 (coding exon 2) of the LPAR1 gene. This alteration results from a T to C substitution at nucleotide position 317, causing the methionine (M) at amino acid position 106 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_001351411.2(LPAR1):c.317T>C (p.Met106Thr)
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.
(1)
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.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001351411.2(LPAR1):c.317T>C (p.Met106Thr)
Variation ID: 2252538 Accession: VCV002252538.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 9q31.3 9: 110941897 (GRCh38) [ NCBI UCSC ] 9: 113704177 (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 8, 2023 May 1, 2024 Sep 27, 2021 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001351411.2:c.317T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001338340.1:p.Met106Thr missense NM_001351397.2:c.317T>C NP_001338326.1:p.Met106Thr missense NM_001351398.2:c.317T>C NP_001338327.1:p.Met106Thr missense NM_001351399.2:c.317T>C NP_001338328.1:p.Met106Thr missense NM_001351400.2:c.317T>C NP_001338329.1:p.Met106Thr missense NM_001351401.2:c.317T>C NP_001338330.1:p.Met106Thr missense NM_001351402.2:c.317T>C NP_001338331.1:p.Met106Thr missense NM_001351403.2:c.317T>C NP_001338332.1:p.Met106Thr missense NM_001351404.2:c.317T>C NP_001338333.1:p.Met106Thr missense NM_001351405.2:c.317T>C NP_001338334.1:p.Met106Thr missense NM_001351406.2:c.317T>C NP_001338335.1:p.Met106Thr missense NM_001351407.2:c.317T>C NP_001338336.1:p.Met106Thr missense NM_001351408.2:c.317T>C NP_001338337.1:p.Met106Thr missense NM_001351409.2:c.317T>C NP_001338338.1:p.Met106Thr missense NM_001351410.2:c.317T>C NP_001338339.1:p.Met106Thr missense NM_001351412.2:c.317T>C NP_001338341.1:p.Met106Thr missense NM_001351413.2:c.317T>C NP_001338342.1:p.Met106Thr missense NM_001351414.2:c.317T>C NP_001338343.1:p.Met106Thr missense NM_001351415.2:c.317T>C NP_001338344.1:p.Met106Thr missense NM_001351416.2:c.317T>C NP_001338345.1:p.Met106Thr missense NM_001351417.2:c.317T>C NP_001338346.1:p.Met106Thr missense NM_001351418.2:c.317T>C NP_001338347.1:p.Met106Thr missense NM_001351419.2:c.317T>C NP_001338348.1:p.Met106Thr missense NM_001351420.2:c.317T>C NP_001338349.1:p.Met106Thr missense NM_001387470.1:c.317T>C NP_001374399.1:p.Met106Thr missense NM_001387471.1:c.317T>C NP_001374400.1:p.Met106Thr missense NM_001387472.1:c.317T>C NP_001374401.1:p.Met106Thr missense NM_001387473.1:c.317T>C NP_001374402.1:p.Met106Thr missense NM_001387474.1:c.317T>C NP_001374403.1:p.Met106Thr missense NM_001387475.1:c.317T>C NP_001374404.1:p.Met106Thr missense NM_001387476.1:c.317T>C NP_001374405.1:p.Met106Thr missense NM_001387477.1:c.317T>C NP_001374406.1:p.Met106Thr missense NM_001387478.1:c.317T>C NP_001374407.1:p.Met106Thr missense NM_001387479.1:c.317T>C NP_001374408.1:p.Met106Thr missense NM_001387480.1:c.317T>C NP_001374409.1:p.Met106Thr missense NM_001387481.1:c.317T>C NP_001374410.1:p.Met106Thr missense NM_001387482.1:c.317T>C NP_001374411.1:p.Met106Thr missense NM_001387483.1:c.317T>C NP_001374412.1:p.Met106Thr missense NM_001387484.1:c.317T>C NP_001374413.1:p.Met106Thr missense NM_001387485.1:c.317T>C NP_001374414.1:p.Met106Thr missense NM_001387486.1:c.317T>C NP_001374415.1:p.Met106Thr missense NM_001387487.1:c.317T>C NP_001374416.1:p.Met106Thr missense NM_001387488.1:c.317T>C NP_001374417.1:p.Met106Thr missense NM_001387489.1:c.317T>C NP_001374418.1:p.Met106Thr missense NM_001387490.1:c.317T>C NP_001374419.1:p.Met106Thr missense NM_001387491.1:c.317T>C NP_001374420.1:p.Met106Thr missense NM_001387492.1:c.317T>C NP_001374421.1:p.Met106Thr missense NM_001387493.1:c.317T>C NP_001374422.1:p.Met106Thr missense NM_001387494.1:c.317T>C NP_001374423.1:p.Met106Thr missense NM_001387495.1:c.317T>C NP_001374424.1:p.Met106Thr missense NM_001387496.1:c.317T>C NP_001374425.1:p.Met106Thr missense NM_001387497.1:c.317T>C NP_001374426.1:p.Met106Thr missense NM_001387498.1:c.317T>C NP_001374427.1:p.Met106Thr missense NM_001387501.1:c.317T>C NP_001374430.1:p.Met106Thr missense NM_001387502.1:c.317T>C NP_001374431.1:p.Met106Thr missense NM_001387503.1:c.317T>C NP_001374432.1:p.Met106Thr missense NM_001387504.1:c.317T>C NP_001374433.1:p.Met106Thr missense NM_001387505.1:c.317T>C NP_001374434.1:p.Met106Thr missense NM_001387506.1:c.317T>C NP_001374435.1:p.Met106Thr missense NM_001387507.1:c.317T>C NP_001374436.1:p.Met106Thr missense NM_001387508.1:c.317T>C NP_001374437.1:p.Met106Thr missense NM_001387509.1:c.317T>C NP_001374438.1:p.Met106Thr missense NM_001387510.1:c.317T>C NP_001374439.1:p.Met106Thr missense NM_001387511.1:c.317T>C NP_001374440.1:p.Met106Thr missense NM_001387512.1:c.317T>C NP_001374441.1:p.Met106Thr missense NM_001387513.1:c.317T>C NP_001374442.1:p.Met106Thr missense NM_001387514.1:c.317T>C NP_001374443.1:p.Met106Thr missense NM_001387515.1:c.317T>C NP_001374444.1:p.Met106Thr missense NM_001387516.1:c.263T>C NP_001374445.1:p.Met88Thr missense NM_001387517.1:c.263T>C NP_001374446.1:p.Met88Thr missense NM_001387518.1:c.263T>C NP_001374447.1:p.Met88Thr missense NM_001387519.1:c.317T>C NP_001374448.1:p.Met106Thr missense NM_001387520.1:c.317T>C NP_001374449.1:p.Met106Thr missense NM_001387521.1:c.317T>C NP_001374450.1:p.Met106Thr missense NM_001401.5:c.317T>C NP_001392.2:p.Met106Thr missense NM_057159.4:c.317T>C NP_476500.1:p.Met106Thr missense NC_000009.12:g.110941897A>G NC_000009.11:g.113704177A>G - Protein change
- M88T, M106T
- Other names
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- Canonical SPDI
- NC_000009.12:110941896:A: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.
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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. |
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| LPAR1 | - | - |
GRCh38 GRCh37 |
19 | 53 | |
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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Sep 27, 2021 | RCV004113799.1 |
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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Uncertain significance
(Sep 27, 2021)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV003584398.2
First in ClinVar: Feb 07, 2023 Last updated: May 01, 2024 |
Comment:
The c.317T>C (p.M106T) alteration is located in exon 4 (coding exon 2) of the LPAR1 gene. This alteration results from a T to C substitution … (more)
The c.317T>C (p.M106T) alteration is located in exon 4 (coding exon 2) of the LPAR1 gene. This alteration results from a T to C substitution at nucleotide position 317, causing the methionine (M) at amino acid position 106 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
|
Comment:
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:
The c.317T>C (p.M106T) alteration is located in exon 4 (coding exon 2) of the LPAR1 gene. This alteration results from a T to C substitution at nucleotide position 317, causing the methionine (M) at amino acid position 106 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
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 Nov 25, 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.