This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
ClinVar Genomic variation as it relates to human health
NM_001368894.2(PAX6):c.1266C>T (p.Pro422=)
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.
(2)
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 benign
2
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.1266C>T (p.Pro422=)
Variation ID: 2078141 Accession: VCV002078141.4
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11p13 11: 31789979 (GRCh38) [ NCBI UCSC ] 11: 31811527 (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 Oct 8, 2024 Jul 18, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001368894.2:c.1266C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001355823.1:p.Pro422= synonymous NM_019040.5:c.*6455G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
3 prime UTR NM_000280.6:c.1224C>T NP_000271.1:p.Pro408= synonymous NM_001127612.3:c.1224C>T NP_001121084.1:p.Pro408= synonymous NM_001258462.3:c.1266C>T NP_001245391.1:p.Pro422= synonymous NM_001258463.2:c.1266C>T NP_001245392.1:p.Pro422= synonymous NM_001258464.2:c.1224C>T NP_001245393.1:p.Pro408= synonymous NM_001258465.3:c.1224C>T NP_001245394.1:p.Pro408= synonymous NM_001288725.2:c.*6441G>A 3 prime UTR NM_001288726.2:c.*6550G>A 3 prime UTR NM_001310158.2:c.1266C>T NP_001297087.1:p.Pro422= synonymous NM_001310160.2:c.816C>T NP_001297089.1:p.Pro272= synonymous NM_001310161.3:c.816C>T NP_001297090.1:p.Pro272= synonymous NM_001368887.2:c.1224C>T NP_001355816.1:p.Pro408= synonymous NM_001368888.2:c.1224C>T NP_001355817.1:p.Pro408= synonymous NM_001368889.2:c.1224C>T NP_001355818.1:p.Pro408= synonymous NM_001368890.2:c.1224C>T NP_001355819.1:p.Pro408= synonymous NM_001368891.2:c.1224C>T NP_001355820.1:p.Pro408= synonymous NM_001368892.2:c.1266C>T NP_001355821.1:p.Pro422= synonymous NM_001368893.2:c.1266C>T NP_001355822.1:p.Pro422= synonymous NM_001368899.2:c.816C>T NP_001355828.1:p.Pro272= synonymous NM_001368900.2:c.816C>T NP_001355829.1:p.Pro272= synonymous NM_001368901.2:c.816C>T NP_001355830.1:p.Pro272= synonymous NM_001368902.2:c.816C>T NP_001355831.1:p.Pro272= synonymous NM_001368903.2:c.816C>T NP_001355832.1:p.Pro272= synonymous NM_001368904.2:c.816C>T NP_001355833.1:p.Pro272= synonymous NM_001368905.2:c.816C>T NP_001355834.1:p.Pro272= synonymous NM_001368906.2:c.816C>T NP_001355835.1:p.Pro272= synonymous NM_001368907.2:c.816C>T NP_001355836.1:p.Pro272= synonymous NM_001368908.2:c.816C>T NP_001355837.1:p.Pro272= synonymous NM_001368909.2:c.816C>T NP_001355838.1:p.Pro272= synonymous NM_001368910.2:c.1467C>T NP_001355839.1:p.Pro489= synonymous NM_001368911.2:c.1118C>T NP_001355840.1:p.Pro373Leu missense NM_001368912.2:c.1115C>T NP_001355841.1:p.Pro372Leu missense NM_001368913.2:c.1115C>T NP_001355842.1:p.Pro372Leu missense NM_001368914.2:c.1115C>T NP_001355843.1:p.Pro372Leu missense NM_001368915.2:c.1073C>T NP_001355844.1:p.Pro358Leu missense NM_001368916.2:c.1073C>T NP_001355845.1:p.Pro358Leu missense NM_001368917.2:c.1073C>T NP_001355846.1:p.Pro358Leu missense NM_001368918.2:c.1341C>T NP_001355847.1:p.Pro447= synonymous NM_001368919.2:c.1341C>T NP_001355848.1:p.Pro447= synonymous NM_001368920.2:c.1299C>T NP_001355849.1:p.Pro433= synonymous NM_001368921.2:c.914C>T NP_001355850.1:p.Pro305Leu missense NM_001368922.2:c.1065C>T NP_001355851.1:p.Pro355= synonymous NM_001368923.2:c.1065C>T NP_001355852.1:p.Pro355= synonymous NM_001368924.2:c.1065C>T NP_001355853.1:p.Pro355= synonymous NM_001368925.2:c.1065C>T NP_001355854.1:p.Pro355= synonymous NM_001368926.2:c.1065C>T NP_001355855.1:p.Pro355= synonymous NM_001368927.2:c.1065C>T NP_001355856.1:p.Pro355= synonymous NM_001368928.2:c.1023C>T NP_001355857.1:p.Pro341= synonymous NM_001368929.2:c.665C>T NP_001355858.1:p.Pro222Leu missense NM_001368930.2:c.621C>T NP_001355859.1:p.Pro207= synonymous NM_001604.6:c.1266C>T NP_001595.2:p.Pro422= synonymous NR_160916.2:n.1454C>T non-coding transcript variant NR_160917.2:n.1610C>T non-coding transcript variant NC_000011.10:g.31789979G>A NC_000011.9:g.31811527G>A NG_008679.1:g.32983C>T NG_034086.2:g.285214G>A LRG_720:g.32983C>T LRG_720t1:c.1224C>T LRG_720p1:p.Pro408= - Protein change
- P358L, P222L, P373L, P305L, P372L
- Other names
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- Canonical SPDI
- NC_000011.10:31789978: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
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 |
698 | 902 | |
| 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 benign (1) |
criteria provided, single submitter
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Jul 18, 2023 | RCV002988479.3 | |
|
PAX6-related disorder
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Likely benign (1) |
no assertion criteria provided
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Nov 17, 2020 | RCV004536509.2 |
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 benign
(Jul 18, 2023)
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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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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003291726.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 28, 2024 |
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Likely benign
(Nov 17, 2020)
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no assertion criteria provided
Method: clinical testing
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PAX6-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004712813.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
|
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:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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 this variant ...
HelpRecord last updated Nov 25, 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.