NM_001368894.2(PAX6):c.1309dup (p.Ter437LeuextTer?) AND Aniridia 1

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 28, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000853307.2

Allele description [Variation Report for NM_001368894.2(PAX6):c.1309dup (p.Ter437LeuextTer?)]

NM_001368894.2(PAX6):c.1309dup (p.Ter437LeuextTer?)

Genes:

ELP4:elongator acetyltransferase complex subunit 4 [Gene - OMIM - HGNC]
PAX6:paired box 6 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_001368894.2(PAX6):c.1309dup (p.Ter437LeuextTer?)

HGVS:

NC_000011.10:g.31789936dup
NG_008679.1:g.33026dup
NG_034086.2:g.285171dup
NM_000280.6:c.1267dup
NM_001127612.3:c.1267dup
NM_001258462.3:c.1309dup
NM_001258463.2:c.1309dup
NM_001258464.2:c.1267dup
NM_001258465.3:c.1267dup
NM_001288725.2:c.*6398dup
NM_001288726.2:c.*6507dup
NM_001310158.2:c.1309dup
NM_001310160.2:c.859dup
NM_001310161.3:c.859dup
NM_001368887.2:c.1267dup
NM_001368888.2:c.1267dup
NM_001368889.2:c.1267dup
NM_001368890.2:c.1267dup
NM_001368891.2:c.1267dup
NM_001368892.2:c.1309dup
NM_001368893.2:c.1309dup
NM_001368894.2:c.1309dupMANE SELECT
NM_001368899.2:c.859dup
NM_001368900.2:c.859dup
NM_001368901.2:c.859dup
NM_001368902.2:c.859dup
NM_001368903.2:c.859dup
NM_001368904.2:c.859dup
NM_001368905.2:c.859dup
NM_001368906.2:c.859dup
NM_001368907.2:c.859dup
NM_001368908.2:c.859dup
NM_001368909.2:c.859dup
NM_001368910.2:c.1510dup
NM_001368911.2:c.1161dup
NM_001368912.2:c.1158dup
NM_001368913.2:c.1158dup
NM_001368914.2:c.1158dup
NM_001368915.2:c.1116dup
NM_001368916.2:c.1116dup
NM_001368917.2:c.1116dup
NM_001368918.2:c.1384dup
NM_001368919.2:c.1384dup
NM_001368920.2:c.1342dup
NM_001368921.2:c.957dup
NM_001368922.2:c.1108dup
NM_001368923.2:c.1108dup
NM_001368924.2:c.1108dup
NM_001368925.2:c.1108dup
NM_001368926.2:c.1108dup
NM_001368927.2:c.1108dup
NM_001368928.2:c.1066dup
NM_001368929.2:c.708dup
NM_001368930.2:c.664dup
NM_001604.6:c.1309dup
NM_019040.5:c.*6412dupMANE SELECT
NP_000271.1:p.Ter423LeuextTer?
NP_000271.1:p.Ter423Leufs
NP_001121084.1:p.Ter423LeuextTer?
NP_001245391.1:p.Ter437LeuextTer?
NP_001245392.1:p.Ter437LeuextTer?
NP_001245393.1:p.Ter423LeuextTer?
NP_001245394.1:p.Ter423LeuextTer?
NP_001297087.1:p.Ter437LeuextTer?
NP_001297089.1:p.Ter287LeuextTer?
NP_001297090.1:p.Ter287LeuextTer?
NP_001355816.1:p.Ter423LeuextTer?
NP_001355817.1:p.Ter423LeuextTer?
NP_001355818.1:p.Ter423LeuextTer?
NP_001355819.1:p.Ter423LeuextTer?
NP_001355820.1:p.Ter423LeuextTer?
NP_001355821.1:p.Ter437LeuextTer?
NP_001355822.1:p.Ter437LeuextTer?
NP_001355823.1:p.Ter437LeuextTer?
NP_001355828.1:p.Ter287LeuextTer?
NP_001355829.1:p.Ter287LeuextTer?
NP_001355830.1:p.Ter287LeuextTer?
NP_001355831.1:p.Ter287LeuextTer?
NP_001355832.1:p.Ter287LeuextTer?
NP_001355833.1:p.Ter287LeuextTer?
NP_001355834.1:p.Ter287LeuextTer?
NP_001355835.1:p.Ter287LeuextTer?
NP_001355836.1:p.Ter287LeuextTer?
NP_001355837.1:p.Ter287LeuextTer?
NP_001355838.1:p.Ter287LeuextTer?
NP_001355839.1:p.Ter504LeuextTer?
NP_001355840.1:p.Lys388Ter
NP_001355841.1:p.Lys387Ter
NP_001355842.1:p.Lys387Ter
NP_001355843.1:p.Lys387Ter
NP_001355844.1:p.Lys373Ter
NP_001355845.1:p.Lys373Ter
NP_001355846.1:p.Lys373Ter
NP_001355847.1:p.Ter462LeuextTer?
NP_001355848.1:p.Ter462LeuextTer?
NP_001355849.1:p.Ter448LeuextTer?
NP_001355850.1:p.Lys320Ter
NP_001355851.1:p.Ter370LeuextTer?
NP_001355852.1:p.Ter370LeuextTer?
NP_001355853.1:p.Ter370LeuextTer?
NP_001355854.1:p.Ter370LeuextTer?
NP_001355855.1:p.Ter370LeuextTer?
NP_001355856.1:p.Ter370LeuextTer?
NP_001355857.1:p.Ter356LeuextTer?
NP_001355858.1:p.Lys237Ter
NP_001355859.1:p.Ter222LeuextTer?
NP_001595.2:p.Ter437LeuextTer?
LRG_720t1:c.1267dup
LRG_720:g.33026dup
LRG_720p1:p.Ter423Leufs
NC_000011.9:g.31811484dup
NM_000280.3:c.1267dup
NM_000280.4:c.1267dupT
NM_001258462.1:c.1309dupT
NR_160916.2:n.1497dup
NR_160917.2:n.1653dup

Protein change:

K237*

Links:

dbSNP: rs1592348310

NCBI 1000 Genomes Browser:

rs1592348310

Molecular consequence:

NM_001288725.2:c.*6398dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001288726.2:c.*6507dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_019040.5:c.*6412dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000280.6:c.1267dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127612.3:c.1267dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258462.3:c.1309dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258463.2:c.1309dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258464.2:c.1267dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258465.3:c.1267dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001310158.2:c.1309dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001310160.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001310161.3:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368887.2:c.1267dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368888.2:c.1267dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368889.2:c.1267dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368890.2:c.1267dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368891.2:c.1267dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368892.2:c.1309dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368893.2:c.1309dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368894.2:c.1309dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368899.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368900.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368901.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368902.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368903.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368904.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368905.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368906.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368907.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368908.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368909.2:c.859dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368910.2:c.1510dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368918.2:c.1384dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368919.2:c.1384dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368920.2:c.1342dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368922.2:c.1108dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368923.2:c.1108dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368924.2:c.1108dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368925.2:c.1108dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368926.2:c.1108dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368927.2:c.1108dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368928.2:c.1066dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368930.2:c.664dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001604.6:c.1309dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_160916.2:n.1497dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_160917.2:n.1653dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001368911.2:c.1161dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368912.2:c.1158dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368913.2:c.1158dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368914.2:c.1158dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368915.2:c.1116dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368916.2:c.1116dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368917.2:c.1116dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368921.2:c.957dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368929.2:c.708dup - nonsense - [Sequence Ontology: SO:0001587]
NM_000280.6:c.1267dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001127612.3:c.1267dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001258462.3:c.1309dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001258463.2:c.1309dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001258464.2:c.1267dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001258465.3:c.1267dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001310158.2:c.1309dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001310160.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001310161.3:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368887.2:c.1267dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368888.2:c.1267dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368889.2:c.1267dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368890.2:c.1267dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368891.2:c.1267dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368892.2:c.1309dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368893.2:c.1309dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368894.2:c.1309dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368899.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368900.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368901.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368902.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368903.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368904.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368905.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368906.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368907.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368908.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368909.2:c.859dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368910.2:c.1510dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368918.2:c.1384dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368919.2:c.1384dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368920.2:c.1342dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368922.2:c.1108dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368923.2:c.1108dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368924.2:c.1108dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368925.2:c.1108dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368926.2:c.1108dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368927.2:c.1108dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368928.2:c.1066dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001368930.2:c.664dup - stop lost - [Sequence Ontology: SO:0001578]
NM_001604.6:c.1309dup - stop lost - [Sequence Ontology: SO:0001578]

Observations:

Condition(s)

Name:: Aniridia 1 (AN1)
Identifiers:: MONDO: MONDO:0024507; MedGen: C0344542; Orphanet: 250923; OMIM: 106210

Recent activity

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GSM38498[Accession] (4)
GEO DataSets
654950[uid] (1)
Taxonomy
Peyssonneliales sp. 7 voucher GH0016287 cytochrome oxidase subunit 1 (COX1) gene...
Peyssonneliales sp. 7 voucher GH0016287 cytochrome oxidase subunit 1 (COX1) gene, partial cds; mitochondrial
gi|2429123925|gb|OM902141.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000996161	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 28, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004036017	GeneReviews	no classification provided	not provided	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 19218613, 27381094

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000996161

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 28, 2018)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004036017

GeneReviews

no classification provided

not provided

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Detailed ophthalmologic evaluation of 43 individuals with PAX6 mutations.

Hingorani M, Williamson KA, Moore AT, van Heyningen V.

Invest Ophthalmol Vis Sci. 2009 Jun;50(6):2581-90. doi: 10.1167/iovs.08-2827. Epub 2009 Feb 14.

PubMed [citation]

PMID:: 19218613

See all PubMed Citations (3)

Details of each submission

From Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV000996161.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

This frameshifting variant is found in the stop codon and is expected to extend the protein by 36 amino acids. This variant has been previously reported as a heterozygous change in patients with aniridia (PMID: 10477494, 25555363). It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.1309dupT (p.Ter437LeufsTer37) variant is classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

From GeneReviews, SCV004036017.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 1, 2024

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