ClinVar Genomic variation as it relates to human health
NM_001368894.2(PAX6):c.1086del (p.Ser363fs)
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_001368894.2(PAX6):c.1086del (p.Ser363fs)
Variation ID: 1390086 Accession: VCV001390086.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 11p13 11: 31790849 (GRCh38) [ NCBI UCSC ] 11: 31812397 (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 Mar 28, 2022 Mar 28, 2022 Dec 31, 2020 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001368894.2:c.1086del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001355823.1:p.Ser363fs frameshift NM_000280.6:c.1044del NP_000271.1:p.Ser349fs frameshift NM_001127612.3:c.1044del NP_001121084.1:p.Ser349fs frameshift NM_001258462.3:c.1086del NP_001245391.1:p.Ser363fs frameshift NM_001258463.2:c.1086del NP_001245392.1:p.Ser363fs frameshift NM_001258464.2:c.1044del NP_001245393.1:p.Ser349fs frameshift NM_001258465.3:c.1044del NP_001245394.1:p.Ser349fs frameshift NM_001310158.2:c.1086del NP_001297087.1:p.Ser363fs frameshift NM_001310160.2:c.636del NP_001297089.1:p.Ser213fs frameshift NM_001310161.3:c.636del NP_001297090.1:p.Ser213fs frameshift NM_001368887.2:c.1044del NP_001355816.1:p.Ser349fs frameshift NM_001368888.2:c.1044del NP_001355817.1:p.Ser349fs frameshift NM_001368889.2:c.1044del NP_001355818.1:p.Ser349fs frameshift NM_001368890.2:c.1044del NP_001355819.1:p.Ser349fs frameshift NM_001368891.2:c.1044del NP_001355820.1:p.Ser349fs frameshift NM_001368892.2:c.1086del NP_001355821.1:p.Ser363fs frameshift NM_001368893.2:c.1086del NP_001355822.1:p.Ser363fs frameshift NM_001368899.2:c.636del NP_001355828.1:p.Ser213fs frameshift NM_001368900.2:c.636del NP_001355829.1:p.Ser213fs frameshift NM_001368901.2:c.636del NP_001355830.1:p.Ser213fs frameshift NM_001368902.2:c.636del NP_001355831.1:p.Ser213fs frameshift NM_001368903.2:c.636del NP_001355832.1:p.Ser213fs frameshift NM_001368904.2:c.636del NP_001355833.1:p.Ser213fs frameshift NM_001368905.2:c.636del NP_001355834.1:p.Ser213fs frameshift NM_001368906.2:c.636del NP_001355835.1:p.Ser213fs frameshift NM_001368907.2:c.636del NP_001355836.1:p.Ser213fs frameshift NM_001368908.2:c.636del NP_001355837.1:p.Ser213fs frameshift NM_001368909.2:c.636del NP_001355838.1:p.Ser213fs frameshift NM_001368910.2:c.1287del NP_001355839.1:p.Ser430fs frameshift NM_001368911.2:c.1078-830del intron variant NM_001368912.2:c.1075-830del intron variant NM_001368913.2:c.1075-830del intron variant NM_001368914.2:c.1075-830del intron variant NM_001368915.2:c.1033-830del intron variant NM_001368916.2:c.1033-830del intron variant NM_001368917.2:c.1033-830del intron variant NM_001368918.2:c.1161del NP_001355847.1:p.Ser388fs frameshift NM_001368919.2:c.1161del NP_001355848.1:p.Ser388fs frameshift NM_001368920.2:c.1119del NP_001355849.1:p.Ser374fs frameshift NM_001368921.2:c.874-830del intron variant NM_001368922.2:c.885del NP_001355851.1:p.Ser296fs frameshift NM_001368923.2:c.885del NP_001355852.1:p.Ser296fs frameshift NM_001368924.2:c.885del NP_001355853.1:p.Ser296fs frameshift NM_001368925.2:c.885del NP_001355854.1:p.Ser296fs frameshift NM_001368926.2:c.885del NP_001355855.1:p.Ser296fs frameshift NM_001368927.2:c.885del NP_001355856.1:p.Ser296fs frameshift NM_001368928.2:c.843del NP_001355857.1:p.Ser282fs frameshift NM_001368929.2:c.625-830del intron variant NM_001368930.2:c.441del NP_001355859.1:p.Ser148fs frameshift NM_001604.6:c.1086del NP_001595.2:p.Ser363fs frameshift NR_160917.2:n.1430del non-coding transcript variant NC_000011.10:g.31790852del NC_000011.9:g.31812400del NG_008679.1:g.32113del LRG_720:g.32113del - Protein change
- S148fs, S296fs, S213fs, S282fs, S349fs, S363fs, S374fs, S388fs, S430fs
- Other names
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- Canonical SPDI
- NC_000011.10:31790848:GGGG:GGG
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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.
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- Links
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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PAX6 | Sufficient evidence for dosage pathogenicity | Little evidence for dosage pathogenicity |
GRCh38 GRCh37 |
666 | 868 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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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Pathogenic (1) |
criteria provided, single submitter
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Dec 31, 2020 | RCV001917511.2 |
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
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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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Pathogenic
(Dec 31, 2020)
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criteria provided, single submitter
Method: clinical testing
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Aniridia 1
Irido-corneo-trabecular dysgenesis
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV002160294.1
First in ClinVar: Mar 28, 2022 Last updated: Mar 28, 2022 |
Comment:
This sequence change creates a premature translational stop signal (p.Ser349Alafs*16) in the PAX6 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Ser349Alafs*16) in the PAX6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PAX6 are known to be pathogenic (PMID: 12634864). This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PAX6-related conditions. For these reasons, this variant has been classified as Pathogenic. (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
HelpTitle | Author | Journal | Year | Link |
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Screening for PAX6 gene mutations is consistent with haploinsufficiency as the main mechanism leading to various ocular defects. | Vincent MC | European journal of human genetics : EJHG | 2003 | PMID: 12634864 |
Text-mined citations for rs1592369895 ...
HelpRecord last updated Apr 06, 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.