ClinVar Genomic variation as it relates to human health
NM_001368894.2(PAX6):c.1001_1002del (p.Thr334fs)
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.1001_1002del (p.Thr334fs)
Variation ID: 2137034 Accession: VCV002137034.2
- Type and length
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Microsatellite, 2 bp
- Location
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Cytogenetic: 11p13 11: 31793510-31793511 (GRCh38) [ NCBI UCSC ] 11: 31815058-31815059 (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 Feb 28, 2024 Apr 1, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001368894.2:c.1001_1002del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001355823.1:p.Thr334fs frameshift NM_000280.6:c.959_960del NP_000271.1:p.Thr320fs frameshift NM_001127612.3:c.959_960del NP_001121084.1:p.Thr320fs frameshift NM_001258462.3:c.1001_1002del NP_001245391.1:p.Thr334fs frameshift NM_001258463.2:c.1001_1002del NP_001245392.1:p.Thr334fs frameshift NM_001258464.2:c.959_960del NP_001245393.1:p.Thr320fs frameshift NM_001258465.3:c.959_960del NP_001245394.1:p.Thr320fs frameshift NM_001310158.2:c.1001_1002del NP_001297087.1:p.Thr334fs frameshift NM_001310159.1:c.959_960del NP_001297088.1:p.Thr320fs frameshift NM_001310160.2:c.551_552del NP_001297089.1:p.Thr184fs frameshift NM_001310161.3:c.551_552del NP_001297090.1:p.Thr184fs frameshift NM_001368887.2:c.959_960del NP_001355816.1:p.Thr320fs frameshift NM_001368888.2:c.959_960del NP_001355817.1:p.Thr320fs frameshift NM_001368889.2:c.959_960del NP_001355818.1:p.Thr320fs frameshift NM_001368890.2:c.959_960del NP_001355819.1:p.Thr320fs frameshift NM_001368891.2:c.959_960del NP_001355820.1:p.Thr320fs frameshift NM_001368892.2:c.1001_1002del NP_001355821.1:p.Thr334fs frameshift NM_001368893.2:c.1001_1002del NP_001355822.1:p.Thr334fs frameshift NM_001368899.2:c.551_552del NP_001355828.1:p.Thr184fs frameshift NM_001368900.2:c.551_552del NP_001355829.1:p.Thr184fs frameshift NM_001368901.2:c.551_552del NP_001355830.1:p.Thr184fs frameshift NM_001368902.2:c.551_552del NP_001355831.1:p.Thr184fs frameshift NM_001368903.2:c.551_552del NP_001355832.1:p.Thr184fs frameshift NM_001368904.2:c.551_552del NP_001355833.1:p.Thr184fs frameshift NM_001368905.2:c.551_552del NP_001355834.1:p.Thr184fs frameshift NM_001368906.2:c.551_552del NP_001355835.1:p.Thr184fs frameshift NM_001368907.2:c.551_552del NP_001355836.1:p.Thr184fs frameshift NM_001368908.2:c.551_552del NP_001355837.1:p.Thr184fs frameshift NM_001368909.2:c.551_552del NP_001355838.1:p.Thr184fs frameshift NM_001368910.2:c.1202_1203del NP_001355839.1:p.Thr401fs frameshift NM_001368911.2:c.1004_1005del NP_001355840.1:p.Thr335fs frameshift NM_001368912.2:c.1001_1002del NP_001355841.1:p.Thr334fs frameshift NM_001368913.2:c.1001_1002del NP_001355842.1:p.Thr334fs frameshift NM_001368914.2:c.1001_1002del NP_001355843.1:p.Thr334fs frameshift NM_001368915.2:c.959_960del NP_001355844.1:p.Thr320fs frameshift NM_001368916.2:c.959_960del NP_001355845.1:p.Thr320fs frameshift NM_001368917.2:c.959_960del NP_001355846.1:p.Thr320fs frameshift NM_001368918.2:c.1076_1077del NP_001355847.1:p.Thr359fs frameshift NM_001368919.2:c.1076_1077del NP_001355848.1:p.Thr359fs frameshift NM_001368920.2:c.1034_1035del NP_001355849.1:p.Thr345fs frameshift NM_001368921.2:c.800_801del NP_001355850.1:p.Thr267fs frameshift NM_001368922.2:c.800_801del NP_001355851.1:p.Thr267fs frameshift NM_001368923.2:c.800_801del NP_001355852.1:p.Thr267fs frameshift NM_001368924.2:c.800_801del NP_001355853.1:p.Thr267fs frameshift NM_001368925.2:c.800_801del NP_001355854.1:p.Thr267fs frameshift NM_001368926.2:c.800_801del NP_001355855.1:p.Thr267fs frameshift NM_001368927.2:c.800_801del NP_001355856.1:p.Thr267fs frameshift NM_001368928.2:c.758_759del NP_001355857.1:p.Thr253fs frameshift NM_001368929.2:c.551_552del NP_001355858.1:p.Thr184fs frameshift NM_001368930.2:c.356_357del NP_001355859.1:p.Thr119fs frameshift NM_001604.6:c.1001_1002del NP_001595.2:p.Thr334fs frameshift NR_160916.2:n.1338CA[1] non-coding transcript variant NR_160917.2:n.1343CA[1] non-coding transcript variant NC_000011.10:g.31793511GT[1] NC_000011.9:g.31815059GT[1] NG_008679.1:g.29449CA[1] LRG_720:g.29449CA[1] LRG_720t1:c.956_957AC[1] LRG_720p1:p.Thr320Serfs - Protein change
- T253fs, T335fs, T359fs, T401fs, T267fs, T320fs, T345fs, T184fs, T334fs, T119fs
- Other names
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- Canonical SPDI
- NC_000011.10:31793509:TGTGT:TGT
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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 |
668 | 870 |
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
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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Pathogenic (1) |
criteria provided, single submitter
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Apr 1, 2022 | RCV003037377.2 |
Submissions - Germline
Classification
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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
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
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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
(Apr 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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Aniridia 1
Irido-corneo-trabecular dysgenesis
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV003440259.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 28, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant is also known as c.957-958delCA. This premature translational stop signal has been observed … (more)
For these reasons, this variant has been classified as Pathogenic. This variant is also known as c.957-958delCA. This premature translational stop signal has been observed in individual(s) with aniridia (PMID: 24078574). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Thr320Serfs*20) 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). (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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[Identification of a novel PAX6 mutation in a family with congenital aniridia]. | Li J | Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics | 2013 | PMID: 24078574 |
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 this variant ...
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.