The c.1200delT variant in the PAX6 gene has been reported previously as NT1617delT using alternate nomenclature in association with aniridia (Chao et al., 2003). The deletion causes a frameshift starting with codon Valine 401, changes this amino acid to a Cystine residue and results in protein extension with a Stop codon at position 124 of the new reading frame, denoted p.Val401CysfsX124. The final 22 amino acids are replaced with 123 incorrect amino acids. The variant is not observed in large population cohorts (Lek et al., 2016). In summary, we consider this variant to be likely pathogenic.
ClinVar Genomic variation as it relates to human health
NM_001368894.2(PAX6):c.1242del (p.Val415fs)
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.
Likely pathogenic
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_001368894.2(PAX6):c.1242del (p.Val415fs)
Variation ID: 817624 Accession: VCV000817624.2
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 11p13 11: 31790003 (GRCh38) [ NCBI UCSC ] 11: 31811551 (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 16, 2020 Mar 16, 2020 Jul 11, 2018 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001368894.2:c.1242del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001355823.1:p.Val415fs frameshift NM_019040.5:c.*6479del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
3 prime UTR NM_000280.6:c.1200del NP_000271.1:p.Val401fs frameshift NM_001127612.3:c.1200del NP_001121084.1:p.Val401fs frameshift NM_001258462.3:c.1242del NP_001245391.1:p.Val415fs frameshift NM_001258463.2:c.1242del NP_001245392.1:p.Val415fs frameshift NM_001258464.2:c.1200del NP_001245393.1:p.Val401fs frameshift NM_001258465.3:c.1200del NP_001245394.1:p.Val401fs frameshift NM_001288725.2:c.*6465del 3 prime UTR NM_001288726.2:c.*6574del 3 prime UTR NM_001310158.2:c.1242del NP_001297087.1:p.Val415fs frameshift NM_001310160.2:c.792del NP_001297089.1:p.Val265fs frameshift NM_001310161.3:c.792del NP_001297090.1:p.Val265fs frameshift NM_001368887.2:c.1200del NP_001355816.1:p.Val401fs frameshift NM_001368888.2:c.1200del NP_001355817.1:p.Val401fs frameshift NM_001368889.2:c.1200del NP_001355818.1:p.Val401fs frameshift NM_001368890.2:c.1200del NP_001355819.1:p.Val401fs frameshift NM_001368891.2:c.1200del NP_001355820.1:p.Val401fs frameshift NM_001368892.2:c.1242del NP_001355821.1:p.Val415fs frameshift NM_001368893.2:c.1242del NP_001355822.1:p.Val415fs frameshift NM_001368899.2:c.792del NP_001355828.1:p.Val265fs frameshift NM_001368900.2:c.792del NP_001355829.1:p.Val265fs frameshift NM_001368901.2:c.792del NP_001355830.1:p.Val265fs frameshift NM_001368902.2:c.792del NP_001355831.1:p.Val265fs frameshift NM_001368903.2:c.792del NP_001355832.1:p.Val265fs frameshift NM_001368904.2:c.792del NP_001355833.1:p.Val265fs frameshift NM_001368905.2:c.792del NP_001355834.1:p.Val265fs frameshift NM_001368906.2:c.792del NP_001355835.1:p.Val265fs frameshift NM_001368907.2:c.792del NP_001355836.1:p.Val265fs frameshift NM_001368908.2:c.792del NP_001355837.1:p.Val265fs frameshift NM_001368909.2:c.792del NP_001355838.1:p.Val265fs frameshift NM_001368910.2:c.1443del NP_001355839.1:p.Val482fs frameshift NM_001368911.2:c.1094del NP_001355840.1:p.Val365fs frameshift NM_001368912.2:c.1091del NP_001355841.1:p.Val364fs frameshift NM_001368913.2:c.1091del NP_001355842.1:p.Val364fs frameshift NM_001368914.2:c.1091del NP_001355843.1:p.Val364fs frameshift NM_001368915.2:c.1049del NP_001355844.1:p.Val350fs frameshift NM_001368916.2:c.1049del NP_001355845.1:p.Val350fs frameshift NM_001368917.2:c.1049del NP_001355846.1:p.Val350fs frameshift NM_001368918.2:c.1317del NP_001355847.1:p.Val440fs frameshift NM_001368919.2:c.1317del NP_001355848.1:p.Val440fs frameshift NM_001368920.2:c.1275del NP_001355849.1:p.Val426fs frameshift NM_001368921.2:c.890del NP_001355850.1:p.Val297fs frameshift NM_001368922.2:c.1041del NP_001355851.1:p.Val348fs frameshift NM_001368923.2:c.1041del NP_001355852.1:p.Val348fs frameshift NM_001368924.2:c.1041del NP_001355853.1:p.Val348fs frameshift NM_001368925.2:c.1041del NP_001355854.1:p.Val348fs frameshift NM_001368926.2:c.1041del NP_001355855.1:p.Val348fs frameshift NM_001368927.2:c.1041del NP_001355856.1:p.Val348fs frameshift NM_001368928.2:c.999del NP_001355857.1:p.Val334fs frameshift NM_001368929.2:c.641del NP_001355858.1:p.Val214fs frameshift NM_001368930.2:c.597del NP_001355859.1:p.Val200fs frameshift NM_001604.6:c.1242del NP_001595.2:p.Val415fs frameshift NR_160916.2:n.1430del non-coding transcript variant NR_160917.2:n.1586del non-coding transcript variant NC_000011.10:g.31790003del NC_000011.9:g.31811551del NG_008679.1:g.32959del NG_034086.2:g.285238del LRG_720:g.32959del LRG_720t1:c.1200del LRG_720p1:p.Val401Cysfs - Protein change
- V350fs, V440fs, V482fs, V200fs, V214fs, V297fs, V334fs, V348fs, V415fs, V426fs, V265fs, V364fs, V365fs, V401fs
- Other names
- -
- Canonical SPDI
- NC_000011.10:31790002: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
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. |
|||
| 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. |
|---|---|---|---|---|
| Likely pathogenic (1) |
criteria provided, single submitter
|
Jul 11, 2018 | RCV001008808.2 |
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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|---|---|---|---|---|---|
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Likely pathogenic
(Jul 11, 2018)
|
criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV001168608.1
First in ClinVar: Mar 16, 2020 Last updated: Mar 16, 2020 |
Comment:
The c.1200delT variant in the PAX6 gene has been reported previously as NT1617delT using alternate nomenclature in association with aniridia (Chao et al., 2003). The … (more)
The c.1200delT variant in the PAX6 gene has been reported previously as NT1617delT using alternate nomenclature in association with aniridia (Chao et al., 2003). The deletion causes a frameshift starting with codon Valine 401, changes this amino acid to a Cystine residue and results in protein extension with a Stop codon at position 124 of the new reading frame, denoted p.Val401CysfsX124. The final 22 amino acids are replaced with 123 incorrect amino acids. The variant is not observed in large population cohorts (Lek et al., 2016). In summary, we consider this variant to be likely pathogenic. (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.1200delT variant in the PAX6 gene has been reported previously as NT1617delT using alternate nomenclature in association with aniridia (Chao et al., 2003). The deletion causes a frameshift starting with codon Valine 401, changes this amino acid to a Cystine residue and results in protein extension with a Stop codon at position 124 of the new reading frame, denoted p.Val401CysfsX124. The final 22 amino acids are replaced with 123 incorrect amino acids. The variant is not observed in large population cohorts (Lek et al., 2016). In summary, we consider this variant to be likely pathogenic.
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 rs1592350160 ...
HelpThese citations are identified by LitVar using
the rs number, so they may include citations for more than one variant
at this location. Please review the LitVar results carefully for your
variant of interest.
Record 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.