NM_000280.4(PAX6):c.357+1G>A AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 19, 2016
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:: RCV000078543.3

Allele description

NM_000280.4(PAX6):c.357+1G>A

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_000280.4(PAX6):c.357+1G>A

HGVS:

NC_000011.10:g.31801560C>T
NG_008679.1:g.21402G>A
NM_000280.4:c.357+1G>A
NM_001310160.1:c.-382G>A
LRG_720:g.21402G>A
NC_000011.9:g.31823108C>T
NM_000280.3:c.357+1G>A

Links:

dbSNP: rs398123295

NCBI 1000 Genomes Browser:

rs398123295

Molecular consequence:

NM_001310160.1:c.-382G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000280.4:c.357+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Observations:

Condition(s)

Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000110399	EGL Genetic Diagnostics,Eurofins Clinical Diagnostics	no assertion criteria provided	Pathogenic (Sep 4, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000490692	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Apr 19, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000110399

EGL Genetic Diagnostics,Eurofins Clinical Diagnostics

no assertion criteria provided

Pathogenic
(Sep 4, 2013)

germline

clinical testing

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

SCV000490692

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Apr 19, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	62	not provided	clinical testing

Citations

PubMed

Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data.

Bean LJ, Tinker SW, da Silva C, Hegde MR.

Hum Mutat. 2013 Sep;34(9):1183-8. doi: 10.1002/humu.22364. Epub 2013 Aug 5.

PubMed [citation]

PMID:: 23757202

Details of each submission

From EGL Genetic Diagnostics,Eurofins Clinical Diagnostics, SCV000110399.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	0	not provided	not provided	clinical testing (GTR000503146)	PubMed (1)
2	not provided	0	not provided	not provided	clinical testing	PubMed (1)
3	not provided	0	not provided	not provided	clinical testing	PubMed (1)
4	not provided	0	not provided	not provided	clinical testing	PubMed (1)
5	not provided	0	not provided	not provided	clinical testing	PubMed (1)
6	not provided	0	not provided	not provided	clinical testing	PubMed (1)
7	not provided	0	not provided	not provided	clinical testing	PubMed (1)
8	not provided	1	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	16	not provided	not provided	(GTR000503146)	0	not provided	not provided	not provided
2	germline	unknown	35	not provided	not provided		0	not provided	not provided	not provided
3	germline	unknown	2	not provided	not provided		0	not provided	not provided	not provided
4	germline	unknown	3	not provided	not provided		0	not provided	not provided	not provided
5	germline	unknown	3	not provided	not provided		0	not provided	not provided	not provided
6	germline	unknown	1	not provided	not provided		0	not provided	not provided	not provided
7	germline	unknown	not provided	not provided	not provided		0	not provided	not provided	not provided
8	germline	unknown	2	not provided	not provided		1	not provided	not provided	not provided

From GeneDx, SCV000490692.1

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

Description

The c.357+1 G>A splice site variant in the PAX6 gene has been previously reported in association with aniridia (Hanson et al., 1993; Axton et al., 1997). Both Hanson et al., and Axton et al., performed RT-PCR on isolated RNA and determined that the variant results in the loss of 36 residues. The c.357+1 G>A variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This pathogenic variant destroys the canonical splice donor site in intron 6, and is expected to cause abnormal gene splicing.

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

Last Updated: Feb 13, 2018

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