ClinVar Genomic variation as it relates to human health
NM_001368894.2(PAX6):c.*20_*21del (p.Ter437=)
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.*20_*21del (p.Ter437=)
Variation ID: 1237893 Accession: VCV001237893.6
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 11p13 11: 31789913-31789914 (GRCh38) [ NCBI UCSC ] 11: 31811461-31811462 (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 Sep 12, 2021 Dec 24, 2023 Dec 12, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001368894.2:c.*20_*21del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001355823.1:p.Ter437= no sequence alteration NM_019040.5:c.*6410_*6411del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
3 prime UTR NM_000280.6:c.*20_*21del NP_000271.1:p.Ter423= no sequence alteration NM_001127612.3:c.*20_*21del NP_001121084.1:p.Ter423= no sequence alteration NM_001258462.3:c.*20_*21del NP_001245391.1:p.Ter437= no sequence alteration NM_001258463.2:c.*20_*21del NP_001245392.1:p.Ter437= no sequence alteration NM_001258464.2:c.*20_*21del NP_001245393.1:p.Ter423= no sequence alteration NM_001258465.3:c.*20_*21del NP_001245394.1:p.Ter423= no sequence alteration NM_001288725.2:c.*6396_*6397del 3 prime UTR NM_001288726.2:c.*6505_*6506del 3 prime UTR NM_001310158.2:c.*20_*21del NP_001297087.1:p.Ter437= no sequence alteration NM_001310160.2:c.*20_*21del NP_001297089.1:p.Ter287= no sequence alteration NM_001310161.3:c.*20_*21del NP_001297090.1:p.Ter287= no sequence alteration NM_001368887.2:c.*20_*21del NP_001355816.1:p.Ter423= no sequence alteration NM_001368888.2:c.*20_*21del NP_001355817.1:p.Ter423= no sequence alteration NM_001368889.2:c.*20_*21del NP_001355818.1:p.Ter423= no sequence alteration NM_001368890.2:c.*20_*21del NP_001355819.1:p.Ter423= no sequence alteration NM_001368891.2:c.*20_*21del NP_001355820.1:p.Ter423= no sequence alteration NM_001368892.2:c.*20_*21del NP_001355821.1:p.Ter437= no sequence alteration NM_001368893.2:c.*20_*21del NP_001355822.1:p.Ter437= no sequence alteration NM_001368899.2:c.*20_*21del NP_001355828.1:p.Ter287= no sequence alteration NM_001368900.2:c.*20_*21del NP_001355829.1:p.Ter287= no sequence alteration NM_001368901.2:c.*20_*21del NP_001355830.1:p.Ter287= no sequence alteration NM_001368902.2:c.*20_*21del NP_001355831.1:p.Ter287= no sequence alteration NM_001368903.2:c.*20_*21del NP_001355832.1:p.Ter287= no sequence alteration NM_001368904.2:c.*20_*21del NP_001355833.1:p.Ter287= no sequence alteration NM_001368905.2:c.*20_*21del NP_001355834.1:p.Ter287= no sequence alteration NM_001368906.2:c.*20_*21del NP_001355835.1:p.Ter287= no sequence alteration NM_001368907.2:c.*20_*21del NP_001355836.1:p.Ter287= no sequence alteration NM_001368908.2:c.*20_*21del NP_001355837.1:p.Ter287= no sequence alteration NM_001368909.2:c.*20_*21del NP_001355838.1:p.Ter287= no sequence alteration NM_001368910.2:c.*20_*21del NP_001355839.1:p.Ter504= no sequence alteration NM_001368911.2:c.1183_1184del NP_001355840.1:p.Lys395fs frameshift NM_001368912.2:c.1180_1181del NP_001355841.1:p.Lys394fs frameshift NM_001368913.2:c.1180_1181del NP_001355842.1:p.Lys394fs frameshift NM_001368914.2:c.1180_1181del NP_001355843.1:p.Lys394fs frameshift NM_001368915.2:c.1138_1139del NP_001355844.1:p.Lys380fs frameshift NM_001368916.2:c.1138_1139del NP_001355845.1:p.Lys380fs frameshift NM_001368917.2:c.1138_1139del NP_001355846.1:p.Lys380fs frameshift NM_001368918.2:c.*20_*21del NP_001355847.1:p.Ter462= no sequence alteration NM_001368919.2:c.*20_*21del NP_001355848.1:p.Ter462= no sequence alteration NM_001368920.2:c.*20_*21del NP_001355849.1:p.Ter448= no sequence alteration NM_001368921.2:c.979_980del NP_001355850.1:p.Lys327fs frameshift NM_001368922.2:c.*20_*21del NP_001355851.1:p.Ter370= no sequence alteration NM_001368923.2:c.*20_*21del NP_001355852.1:p.Ter370= no sequence alteration NM_001368924.2:c.*20_*21del NP_001355853.1:p.Ter370= no sequence alteration NM_001368925.2:c.*20_*21del NP_001355854.1:p.Ter370= no sequence alteration NM_001368926.2:c.*20_*21del NP_001355855.1:p.Ter370= no sequence alteration NM_001368927.2:c.*20_*21del NP_001355856.1:p.Ter370= no sequence alteration NM_001368928.2:c.*20_*21del NP_001355857.1:p.Ter356= no sequence alteration NM_001368929.2:c.730_731del NP_001355858.1:p.Lys244fs frameshift NM_001368930.2:c.*20_*21del NP_001355859.1:p.Ter222= no sequence alteration NM_001604.6:c.*20_*21del NP_001595.2:p.Ter437= no sequence alteration NR_160916.2:n.1519_1520del non-coding transcript variant NR_160917.2:n.1675_1676del non-coding transcript variant NC_000011.10:g.31789934_31789935del NC_000011.9:g.31811482_31811483del NG_008679.1:g.33048_33049del NG_034086.2:g.285169_285170del LRG_720:g.33048_33049del LRG_720t1:c.1268_1269del LRG_720p1:p.Ter423= - Protein change
- K244fs, K327fs, K380fs, K394fs, K395fs
- Other names
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- Canonical SPDI
- NC_000011.10:31789912:TTTTTTTTTTTTTTTTTTTTTTT:TTTTTTTTTTTTTTTTTTTTT
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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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| PAX6 | Sufficient evidence for dosage pathogenicity | Little evidence for dosage pathogenicity |
GRCh38 GRCh37 |
695 | 899 | |
| ELP4 | - | - |
GRCh38 GRCh37 |
62 | 288 | |
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. |
|---|---|---|---|---|
| Benign (1) |
criteria provided, single submitter
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Aug 19, 2019 | RCV001637441.5 | |
| Likely benign (1) |
criteria provided, single submitter
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Sep 5, 2023 | RCV003327301.3 | |
| Benign (1) |
criteria provided, single submitter
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Dec 12, 2023 | RCV003451835.2 |
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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Benign
(Aug 19, 2019)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001850688.1
First in ClinVar: Sep 12, 2021 Last updated: Sep 12, 2021 |
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Likely benign
(Sep 05, 2023)
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criteria provided, single submitter
Method: clinical testing
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PAX6-related ocular dysgenesis
(Autosomal dominant inheritance)
Affected status: no
Allele origin:
germline
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Intergen, Intergen Genetics and Rare Diseases Diagnosis Center
Accession: SCV004031426.1
First in ClinVar: Sep 16, 2023 Last updated: Sep 16, 2023 |
Comment on evidence:
The individial did not have any feature consistent with the phenotypes caused by pathogenic variants of the gene. Therefore the variant is classified as "likeşy … (more)
The individial did not have any feature consistent with the phenotypes caused by pathogenic variants of the gene. Therefore the variant is classified as "likeşy benign". (less)
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Benign
(Dec 12, 2023)
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criteria provided, single submitter
Method: research
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Coloboma of optic nerve
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004183321.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
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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
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 rs759391101 ...
HelpRecord last updated Sep 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.