NM_001368894.2(PAX6):c.1103dup (p.Tyr368Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 28, 2022
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:: RCV003032812.3

Allele description [Variation Report for NM_001368894.2(PAX6):c.1103dup (p.Tyr368Ter)]

NM_001368894.2(PAX6):c.1103dup (p.Tyr368Ter)

Gene:

PAX6:paired box 6 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_001368894.2(PAX6):c.1103dup (p.Tyr368Ter)

HGVS:

NC_000011.10:g.31790832dup
NG_008679.1:g.32130dup
NG_034086.2:g.286067dup
NM_000280.6:c.1061dup
NM_001127612.3:c.1061dup
NM_001258462.3:c.1103dup
NM_001258463.2:c.1103dup
NM_001258464.2:c.1061dup
NM_001258465.3:c.1061dup
NM_001310158.2:c.1103dup
NM_001310160.2:c.653dup
NM_001310161.3:c.653dup
NM_001368887.2:c.1061dup
NM_001368888.2:c.1061dup
NM_001368889.2:c.1061dup
NM_001368890.2:c.1061dup
NM_001368891.2:c.1061dup
NM_001368892.2:c.1103dup
NM_001368893.2:c.1103dup
NM_001368894.2:c.1103dupMANE SELECT
NM_001368899.2:c.653dup
NM_001368900.2:c.653dup
NM_001368901.2:c.653dup
NM_001368902.2:c.653dup
NM_001368903.2:c.653dup
NM_001368904.2:c.653dup
NM_001368905.2:c.653dup
NM_001368906.2:c.653dup
NM_001368907.2:c.653dup
NM_001368908.2:c.653dup
NM_001368909.2:c.653dup
NM_001368910.2:c.1304dup
NM_001368911.2:c.1078-813dup
NM_001368912.2:c.1075-813dup
NM_001368913.2:c.1075-813dup
NM_001368914.2:c.1075-813dup
NM_001368915.2:c.1033-813dup
NM_001368916.2:c.1033-813dup
NM_001368917.2:c.1033-813dup
NM_001368918.2:c.1178dup
NM_001368919.2:c.1178dup
NM_001368920.2:c.1136dup
NM_001368921.2:c.874-813dup
NM_001368922.2:c.902dup
NM_001368923.2:c.902dup
NM_001368924.2:c.902dup
NM_001368925.2:c.902dup
NM_001368926.2:c.902dup
NM_001368927.2:c.902dup
NM_001368928.2:c.860dup
NM_001368929.2:c.625-813dup
NM_001368930.2:c.458dup
NM_001604.6:c.1103dup
NP_000271.1:p.Tyr354Ter
NP_000271.1:p.Tyr354Terfs
NP_001121084.1:p.Tyr354Ter
NP_001245391.1:p.Tyr368Ter
NP_001245392.1:p.Tyr368Ter
NP_001245393.1:p.Tyr354Ter
NP_001245394.1:p.Tyr354Ter
NP_001297087.1:p.Tyr368Ter
NP_001297089.1:p.Tyr218Ter
NP_001297090.1:p.Tyr218Ter
NP_001355816.1:p.Tyr354Ter
NP_001355817.1:p.Tyr354Ter
NP_001355818.1:p.Tyr354Ter
NP_001355819.1:p.Tyr354Ter
NP_001355820.1:p.Tyr354Ter
NP_001355821.1:p.Tyr368Ter
NP_001355822.1:p.Tyr368Ter
NP_001355823.1:p.Tyr368Ter
NP_001355828.1:p.Tyr218Ter
NP_001355829.1:p.Tyr218Ter
NP_001355830.1:p.Tyr218Ter
NP_001355831.1:p.Tyr218Ter
NP_001355832.1:p.Tyr218Ter
NP_001355833.1:p.Tyr218Ter
NP_001355834.1:p.Tyr218Ter
NP_001355835.1:p.Tyr218Ter
NP_001355836.1:p.Tyr218Ter
NP_001355837.1:p.Tyr218Ter
NP_001355838.1:p.Tyr218Ter
NP_001355839.1:p.Tyr435Ter
NP_001355847.1:p.Tyr393Ter
NP_001355848.1:p.Tyr393Ter
NP_001355849.1:p.Tyr379Ter
NP_001355851.1:p.Tyr301Ter
NP_001355852.1:p.Tyr301Ter
NP_001355853.1:p.Tyr301Ter
NP_001355854.1:p.Tyr301Ter
NP_001355855.1:p.Tyr301Ter
NP_001355856.1:p.Tyr301Ter
NP_001355857.1:p.Tyr287Ter
NP_001355859.1:p.Tyr153Ter
NP_001595.2:p.Tyr368Ter
LRG_720t1:c.1061dup
LRG_720:g.32130dup
LRG_720p1:p.Tyr354Terfs
NC_000011.9:g.31812379_31812380insT
NC_000011.9:g.31812380dup
NM_000280.3:c.1061dup
NR_160917.2:n.1447dup

Protein change:

Y153*

Molecular consequence:

NM_001368911.2:c.1078-813dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001368912.2:c.1075-813dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001368913.2:c.1075-813dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001368914.2:c.1075-813dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001368915.2:c.1033-813dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001368916.2:c.1033-813dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001368917.2:c.1033-813dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001368921.2:c.874-813dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001368929.2:c.625-813dup - intron variant - [Sequence Ontology: SO:0001627]
NR_160917.2:n.1447dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000280.6:c.1061dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001127612.3:c.1061dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001258462.3:c.1103dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001258463.2:c.1103dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001258464.2:c.1061dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001258465.3:c.1061dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001310158.2:c.1103dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001310160.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001310161.3:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368887.2:c.1061dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368888.2:c.1061dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368889.2:c.1061dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368890.2:c.1061dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368891.2:c.1061dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368892.2:c.1103dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368893.2:c.1103dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368894.2:c.1103dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368899.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368900.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368901.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368902.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368903.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368904.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368905.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368906.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368907.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368908.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368909.2:c.653dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368910.2:c.1304dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368918.2:c.1178dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368919.2:c.1178dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368920.2:c.1136dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368922.2:c.902dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368923.2:c.902dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368924.2:c.902dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368925.2:c.902dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368926.2:c.902dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368927.2:c.902dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368928.2:c.860dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001368930.2:c.458dup - nonsense - [Sequence Ontology: SO:0001587]
NM_001604.6:c.1103dup - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

Name:: Irido-corneo-trabecular dysgenesis (ASGD5)
Synonyms:: ANTERIOR SEGMENT DYSGENESIS 5
Identifiers:: MONDO: MONDO:0011414; MedGen: C0344559; Orphanet: 708; OMIM: 604229; Human Phenotype Ontology: HP:0000659

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SRS1613990 (3)
SRA
Homo sapiens poly(A) binding protein interacting protein 2B (PAIP2B), mRNA
Homo sapiens poly(A) binding protein interacting protein 2B (PAIP2B), mRNA
gi|148235698|ref|NM_020459.1|

Nucleotide
SRP083158 (1)
SRA
Glycosyltransferase [Streptococcus suis]
Glycosyltransferase [Streptococcus suis]
gi|1139490665|gb|APZ79396.1|

Protein
LIPM lipase family member M [Homo sapiens]
LIPM lipase family member M [Homo sapiens]
Gene ID:340654

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003330983	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 28, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12634864, 21850189, 32360764, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003330983

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 28, 2022)

germline

clinical testing

PubMed (4)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Screening for PAX6 gene mutations is consistent with haploinsufficiency as the main mechanism leading to various ocular defects.

Vincent MC, Pujo AL, Olivier D, Calvas P.

Eur J Hum Genet. 2003 Feb;11(2):163-9.

PubMed [citation]

PMID:: 12634864

Mutation spectrum of PAX6 in Chinese patients with aniridia.

Zhang X, Wang P, Li S, Xiao X, Guo X, Zhang Q.

Mol Vis. 2011;17:2139-47. Epub 2011 Aug 11.

PubMed [citation]

PMID:: 21850189
PMCID:: PMC3156780

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003330983.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Tyr354*) 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). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with aniridia (PMID: 21850189, 32360764). For these reasons, this variant has been classified as Pathogenic.

#	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 29, 2024

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