NM_001368894.2(PAX6):c.496C>T (p.Gln166Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 10, 2023
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:: RCV003783564.2

Allele description [Variation Report for NM_001368894.2(PAX6):c.496C>T (p.Gln166Ter)]

NM_001368894.2(PAX6):c.496C>T (p.Gln166Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_001368894.2(PAX6):c.496C>T (p.Gln166Ter)

HGVS:

NC_000011.10:g.31800760G>A
NG_008679.1:g.22202C>T
NM_000280.6:c.454C>T
NM_001127612.3:c.454C>T
NM_001258462.3:c.496C>T
NM_001258463.2:c.496C>T
NM_001258464.2:c.454C>T
NM_001258465.3:c.454C>T
NM_001310158.2:c.496C>T
NM_001310159.1:c.454C>T
NM_001310160.2:c.46C>T
NM_001310161.3:c.46C>T
NM_001368887.2:c.454C>T
NM_001368888.2:c.454C>T
NM_001368889.2:c.454C>T
NM_001368890.2:c.454C>T
NM_001368891.2:c.454C>T
NM_001368892.2:c.496C>T
NM_001368893.2:c.496C>T
NM_001368894.2:c.496C>TMANE SELECT
NM_001368899.2:c.46C>T
NM_001368900.2:c.46C>T
NM_001368901.2:c.46C>T
NM_001368902.2:c.46C>T
NM_001368903.2:c.46C>T
NM_001368904.2:c.46C>T
NM_001368905.2:c.46C>T
NM_001368906.2:c.46C>T
NM_001368907.2:c.46C>T
NM_001368908.2:c.46C>T
NM_001368909.2:c.46C>T
NM_001368910.2:c.697C>T
NM_001368911.2:c.499C>T
NM_001368912.2:c.496C>T
NM_001368913.2:c.496C>T
NM_001368914.2:c.496C>T
NM_001368915.2:c.454C>T
NM_001368916.2:c.454C>T
NM_001368917.2:c.454C>T
NM_001368918.2:c.571C>T
NM_001368919.2:c.571C>T
NM_001368920.2:c.529C>T
NM_001368921.2:c.295C>T
NM_001368922.2:c.295C>T
NM_001368923.2:c.295C>T
NM_001368924.2:c.295C>T
NM_001368925.2:c.295C>T
NM_001368926.2:c.295C>T
NM_001368927.2:c.295C>T
NM_001368928.2:c.253C>T
NM_001368929.2:c.46C>T
NM_001604.6:c.496C>T
NP_000271.1:p.Gln152Ter
NP_000271.1:p.Gln152Ter
NP_001121084.1:p.Gln152Ter
NP_001245391.1:p.Gln166Ter
NP_001245392.1:p.Gln166Ter
NP_001245393.1:p.Gln152Ter
NP_001245394.1:p.Gln152Ter
NP_001297087.1:p.Gln166Ter
NP_001297088.1:p.Gln152Ter
NP_001297089.1:p.Gln16Ter
NP_001297090.1:p.Gln16Ter
NP_001355816.1:p.Gln152Ter
NP_001355817.1:p.Gln152Ter
NP_001355818.1:p.Gln152Ter
NP_001355819.1:p.Gln152Ter
NP_001355820.1:p.Gln152Ter
NP_001355821.1:p.Gln166Ter
NP_001355822.1:p.Gln166Ter
NP_001355823.1:p.Gln166Ter
NP_001355828.1:p.Gln16Ter
NP_001355829.1:p.Gln16Ter
NP_001355830.1:p.Gln16Ter
NP_001355831.1:p.Gln16Ter
NP_001355832.1:p.Gln16Ter
NP_001355833.1:p.Gln16Ter
NP_001355834.1:p.Gln16Ter
NP_001355835.1:p.Gln16Ter
NP_001355836.1:p.Gln16Ter
NP_001355837.1:p.Gln16Ter
NP_001355838.1:p.Gln16Ter
NP_001355839.1:p.Gln233Ter
NP_001355840.1:p.Gln167Ter
NP_001355841.1:p.Gln166Ter
NP_001355842.1:p.Gln166Ter
NP_001355843.1:p.Gln166Ter
NP_001355844.1:p.Gln152Ter
NP_001355845.1:p.Gln152Ter
NP_001355846.1:p.Gln152Ter
NP_001355847.1:p.Gln191Ter
NP_001355848.1:p.Gln191Ter
NP_001355849.1:p.Gln177Ter
NP_001355850.1:p.Gln99Ter
NP_001355851.1:p.Gln99Ter
NP_001355852.1:p.Gln99Ter
NP_001355853.1:p.Gln99Ter
NP_001355854.1:p.Gln99Ter
NP_001355855.1:p.Gln99Ter
NP_001355856.1:p.Gln99Ter
NP_001355857.1:p.Gln85Ter
NP_001355858.1:p.Gln16Ter
NP_001595.2:p.Gln166Ter
LRG_720t1:c.454C>T
LRG_720:g.22202C>T
LRG_720p1:p.Gln152Ter
NC_000011.9:g.31822308G>A
NM_000280.3:c.454C>T
NR_160916.2:n.918C>T
NR_160917.2:n.923C>T

Protein change:

Q152*

Molecular consequence:

NR_160916.2:n.918C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_160917.2:n.923C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000280.6:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001127612.3:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001258462.3:c.496C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001258463.2:c.496C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001258464.2:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001258465.3:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001310158.2:c.496C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001310159.1:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001310160.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001310161.3:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368887.2:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368888.2:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368889.2:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368890.2:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368891.2:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368892.2:c.496C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368893.2:c.496C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368894.2:c.496C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368899.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368900.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368901.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368902.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368903.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368904.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368905.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368906.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368907.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368908.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368909.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368910.2:c.697C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368911.2:c.499C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368912.2:c.496C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368913.2:c.496C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368914.2:c.496C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368915.2:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368916.2:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368917.2:c.454C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368918.2:c.571C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368919.2:c.571C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368920.2:c.529C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368921.2:c.295C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368922.2:c.295C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368923.2:c.295C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368924.2:c.295C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368925.2:c.295C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368926.2:c.295C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368927.2:c.295C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368928.2:c.253C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001368929.2:c.46C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001604.6:c.496C>T - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004570836	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 10, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12634864, 12552561, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004570836

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 10, 2023)

germline

clinical testing

PubMed (3)
[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

Missense mutations in the DNA-binding region and termination codon in PAX6.

Chao LY, Mishra R, Strong LC, Saunders GF.

Hum Mutat. 2003 Feb;21(2):138-45.

PubMed [citation]

PMID:: 12552561

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004570836.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Gln152*) 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 and foveal hypoplasia (PMID: 12552561). 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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