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NM_001368894.2(PAX6):c.1074+1G>C AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 12, 2021
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:
RCV001946374.3

Allele description [Variation Report for NM_001368894.2(PAX6):c.1074+1G>C]

NM_001368894.2(PAX6):c.1074+1G>C

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.1074+1G>C
HGVS:
  • NC_000011.10:g.31793437C>G
  • NG_008679.1:g.29525G>C
  • NG_159898.1:g.331C>G
  • NM_000280.6:c.1032+1G>C
  • NM_001127612.3:c.1032+1G>C
  • NM_001258462.3:c.1074+1G>C
  • NM_001258463.2:c.1074+1G>C
  • NM_001258464.2:c.1032+1G>C
  • NM_001258465.3:c.1032+1G>C
  • NM_001310158.2:c.1074+1G>C
  • NM_001310159.1:c.1033G>C
  • NM_001310160.2:c.624+1G>C
  • NM_001310161.3:c.624+1G>C
  • NM_001368887.2:c.1032+1G>C
  • NM_001368888.2:c.1032+1G>C
  • NM_001368889.2:c.1032+1G>C
  • NM_001368890.2:c.1032+1G>C
  • NM_001368891.2:c.1032+1G>C
  • NM_001368892.2:c.1074+1G>C
  • NM_001368893.2:c.1074+1G>C
  • NM_001368894.2:c.1074+1G>CMANE SELECT
  • NM_001368899.2:c.624+1G>C
  • NM_001368900.2:c.624+1G>C
  • NM_001368901.2:c.624+1G>C
  • NM_001368902.2:c.624+1G>C
  • NM_001368903.2:c.624+1G>C
  • NM_001368904.2:c.624+1G>C
  • NM_001368905.2:c.624+1G>C
  • NM_001368906.2:c.624+1G>C
  • NM_001368907.2:c.624+1G>C
  • NM_001368908.2:c.624+1G>C
  • NM_001368909.2:c.624+1G>C
  • NM_001368910.2:c.1275+1G>C
  • NM_001368911.2:c.1077+1G>C
  • NM_001368912.2:c.1074+1G>C
  • NM_001368913.2:c.1074+1G>C
  • NM_001368914.2:c.1074+1G>C
  • NM_001368915.2:c.1032+1G>C
  • NM_001368916.2:c.1032+1G>C
  • NM_001368917.2:c.1032+1G>C
  • NM_001368918.2:c.1149+1G>C
  • NM_001368919.2:c.1149+1G>C
  • NM_001368920.2:c.1107+1G>C
  • NM_001368921.2:c.873+1G>C
  • NM_001368922.2:c.873+1G>C
  • NM_001368923.2:c.873+1G>C
  • NM_001368924.2:c.873+1G>C
  • NM_001368925.2:c.873+1G>C
  • NM_001368926.2:c.873+1G>C
  • NM_001368927.2:c.873+1G>C
  • NM_001368928.2:c.831+1G>C
  • NM_001368929.2:c.624+1G>C
  • NM_001368930.2:c.429+1G>C
  • NM_001604.6:c.1074+1G>C
  • NP_001297088.1:p.Val345Leu
  • LRG_720:g.29525G>C
  • NC_000011.9:g.31814985C>G
Protein change:
V345L
Links:
dbSNP: rs1950507886
NCBI 1000 Genomes Browser:
rs1950507886
Molecular consequence:
  • NM_001310159.1:c.1033G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000280.6:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001127612.3:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258462.3:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258463.2:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258464.2:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258465.3:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001310158.2:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001310160.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001310161.3:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368887.2:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368888.2:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368889.2:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368890.2:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368891.2:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368892.2:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368893.2:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368894.2:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368899.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368900.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368901.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368902.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368903.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368904.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368905.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368906.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368907.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368908.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368909.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368910.2:c.1275+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368911.2:c.1077+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368912.2:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368913.2:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368914.2:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368915.2:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368916.2:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368917.2:c.1032+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368918.2:c.1149+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368919.2:c.1149+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368920.2:c.1107+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368921.2:c.873+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368922.2:c.873+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368923.2:c.873+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368924.2:c.873+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368925.2:c.873+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368926.2:c.873+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368927.2:c.873+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368928.2:c.831+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368929.2:c.624+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001368930.2:c.429+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001604.6:c.1074+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002211533Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 12, 2021) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutational analysis of PAX6: 16 novel mutations including 5 missense mutations with a mild aniridia phenotype.

Grønskov K, Rosenberg T, Sand A, Brøndum-Nielsen K.

Eur J Hum Genet. 1999 Apr;7(3):274-86.

PubMed [citation]
PMID:
10234503

Genotype-phenotype correlation of PAX6 gene mutations in aniridia.

Yokoi T, Nishina S, Fukami M, Ogata T, Hosono K, Hotta Y, Azuma N.

Hum Genome Var. 2016;3:15052. doi: 10.1038/hgv.2015.52.

PubMed [citation]
PMID:
27081561
PMCID:
PMC4760117
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002211533.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in skipping of exon 11 and introduces a premature termination codon (PMID: 10234503). The resulting mRNA is expected to undergo nonsense-mediated decay. Disruption of this splice site has been observed in individual(s) with aniridia (PMID: 10234503, 27081561). This variant is not present in population databases (ExAC no frequency). This sequence change affects a donor splice site in intron 11 of the PAX6 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 6, 2024