ClinVar Genomic variation as it relates to human health
NM_014042.3(ANAPC15):c.296C>T (p.Pro99Leu)
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_014042.3(ANAPC15):c.296C>T (p.Pro99Leu)
Variation ID: 306014 Accession: VCV000306014.6
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11q13.4 11: 72110110 (GRCh38) [ NCBI UCSC ] 11: 71821156 (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 Dec 6, 2016 Oct 28, 2023 Jul 25, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_014042.3:c.296C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_054761.1:p.Pro99Leu missense NM_001145308.5:c.*1185G>A 3 prime UTR NM_001145309.4:c.*1185G>A 3 prime UTR NM_001145310.4:c.*1185G>A 3 prime UTR NM_001278485.2:c.296C>T NP_001265414.1:p.Pro99Leu missense NM_001278486.2:c.296C>T NP_001265415.1:p.Pro99Leu missense NM_001278487.2:c.296C>T NP_001265416.1:p.Pro99Leu missense NM_001278488.2:c.296C>T NP_001265417.1:p.Pro99Leu missense NM_001278489.2:c.296C>T NP_001265418.1:p.Pro99Leu missense NM_001278490.2:c.296C>T NP_001265419.1:p.Pro99Leu missense NM_001278491.1:c.296C>T NP_001265420.1:p.Pro99Leu missense NM_001278492.2:c.296C>T NP_001265421.1:p.Pro99Leu missense NM_001278493.2:c.296C>T NP_001265422.1:p.Pro99Leu missense NM_001278494.2:c.296C>T NP_001265423.1:p.Pro99Leu missense NM_001330321.2:c.296C>T NP_001317250.1:p.Pro99Leu missense NM_001393427.1:c.296C>T NP_001380356.1:p.Pro99Leu missense NM_001393428.1:c.296C>T NP_001380357.1:p.Pro99Leu missense NM_001393429.1:c.296C>T NP_001380358.1:p.Pro99Leu missense NM_001393430.1:c.296C>T NP_001380359.1:p.Pro99Leu missense NM_001393431.1:c.296C>T NP_001380360.1:p.Pro99Leu missense NM_001393432.1:c.332C>T NP_001380361.1:p.Pro111Leu missense NM_001393433.1:c.332C>T NP_001380362.1:p.Pro111Leu missense NM_001393434.1:c.332C>T NP_001380363.1:p.Pro111Leu missense NM_001393435.1:c.332C>T NP_001380364.1:p.Pro111Leu missense NM_001393436.1:c.332C>T NP_001380365.1:p.Pro111Leu missense NM_001393437.1:c.296C>T NP_001380366.1:p.Pro99Leu missense NM_001393438.1:c.296C>T NP_001380367.1:p.Pro99Leu missense NM_001393439.1:c.296C>T NP_001380368.1:p.Pro99Leu missense NM_001393440.1:c.296C>T NP_001380369.1:p.Pro99Leu missense NM_001393441.1:c.296C>T NP_001380370.1:p.Pro99Leu missense NM_001393442.1:c.296C>T NP_001380371.1:p.Pro99Leu missense NM_001393443.1:c.296C>T NP_001380372.1:p.Pro99Leu missense NM_001393444.1:c.296C>T NP_001380373.1:p.Pro99Leu missense NM_001393445.1:c.296C>T NP_001380374.1:p.Pro99Leu missense NM_001393446.1:c.296C>T NP_001380375.1:p.Pro99Leu missense NM_001393447.1:c.296C>T NP_001380376.1:p.Pro99Leu missense NM_001393448.1:c.296C>T NP_001380377.1:p.Pro99Leu missense NM_001393449.1:c.296C>T NP_001380378.1:p.Pro99Leu missense NM_001393450.1:c.296C>T NP_001380379.1:p.Pro99Leu missense NM_001393451.1:c.296C>T NP_001380380.1:p.Pro99Leu missense NM_001393452.1:c.296C>T NP_001380381.1:p.Pro99Leu missense NM_001393453.1:c.296C>T NP_001380382.1:p.Pro99Leu missense NM_001393454.1:c.296C>T NP_001380383.1:p.Pro99Leu missense NM_001393455.1:c.296C>T NP_001380384.1:p.Pro99Leu missense NM_001393456.1:c.296C>T NP_001380385.1:p.Pro99Leu missense NM_001393457.1:c.296C>T NP_001380386.1:p.Pro99Leu missense NM_001393458.1:c.296C>T NP_001380387.1:p.Pro99Leu missense NM_001393459.1:c.41C>T NP_001380388.1:p.Pro14Leu missense NM_014042.2:c.296C>T NR_171684.1:n.307C>T non-coding transcript variant NR_171685.1:n.307C>T non-coding transcript variant NR_171686.1:n.222C>T non-coding transcript variant NR_171687.1:n.432C>T non-coding transcript variant NC_000011.10:g.72110110G>A NC_000011.9:g.71821156G>A NG_021423.1:g.34775G>A - Protein change
- P99L, P111L, P14L
- Other names
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- Canonical SPDI
- NC_000011.10:72110109: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
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The frequency of the allele represented by this VCV record.
Trans-Omics for Precision Medicine (TOPMed) 0.00013
The Genome Aggregation Database (gnomAD) 0.00016
Exome Aggregation Consortium (ExAC) 0.00011
The Genome Aggregation Database (gnomAD), exomes 0.00010
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00010
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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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ANAPC15 | - | - |
GRCh38 GRCh37 |
- | 112 | |
LRTOMT | - | - |
GRCh38 GRCh37 |
23 | 232 |
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
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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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Jan 13, 2018 | RCV000272780.5 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jul 25, 2023 | RCV003362751.1 |
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
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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
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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
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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
(Jan 13, 2018)
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criteria provided, single submitter
Method: clinical testing
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Autosomal recessive nonsyndromic hearing loss 63
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000373991.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
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)
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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. (less)
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Uncertain significance
(Jul 25, 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: SCV004057445.1
First in ClinVar: Oct 28, 2023 Last updated: Oct 28, 2023 |
Comment:
The c.296C>T (p.P99L) alteration is located in exon 5 (coding exon 3) of the ANAPC15 gene. This alteration results from a C to T substitution … (more)
The c.296C>T (p.P99L) alteration is located in exon 5 (coding exon 3) of the ANAPC15 gene. This alteration results from a C to T substitution at nucleotide position 296, causing the proline (P) at amino acid position 99 to be replaced by a leucine (L). 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 rs531848254 ...
HelpRecord last updated Oct 28, 2023
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.