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NM_001368894.2(PAX6):c.78del (p.Gln27fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 19, 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:
RCV000804957.5

Allele description [Variation Report for NM_001368894.2(PAX6):c.78del (p.Gln27fs)]

NM_001368894.2(PAX6):c.78del (p.Gln27fs)

Gene:
PAX6:paired box 6 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11p13
Genomic location:
Preferred name:
NM_001368894.2(PAX6):c.78del (p.Gln27fs)
HGVS:
  • NC_000011.10:g.31802768del
  • NC_000011.9:g.31824315del
  • NG_008679.1:g.20195del
  • NM_000280.6:c.78del
  • NM_001127612.3:c.78del
  • NM_001258462.3:c.78del
  • NM_001258463.2:c.78del
  • NM_001258464.2:c.78del
  • NM_001258465.3:c.78del
  • NM_001310158.2:c.78del
  • NM_001310159.1:c.78del
  • NM_001310160.2:c.-704del
  • NM_001310161.3:c.-373del
  • NM_001368887.2:c.78del
  • NM_001368888.2:c.78del
  • NM_001368889.2:c.78del
  • NM_001368890.2:c.78del
  • NM_001368891.2:c.78del
  • NM_001368892.2:c.78del
  • NM_001368893.2:c.78del
  • NM_001368894.2:c.78delMANE SELECT
  • NM_001368899.2:c.-331del
  • NM_001368900.2:c.-373del
  • NM_001368901.2:c.-331del
  • NM_001368902.2:c.-662del
  • NM_001368903.2:c.-373del
  • NM_001368904.2:c.-267-991del
  • NM_001368905.2:c.-704del
  • NM_001368906.2:c.-331del
  • NM_001368907.2:c.-331del
  • NM_001368908.2:c.-373del
  • NM_001368909.2:c.-267-991del
  • NM_001368910.2:c.321del
  • NM_001368911.2:c.81del
  • NM_001368912.2:c.78del
  • NM_001368913.2:c.78del
  • NM_001368914.2:c.78del
  • NM_001368915.2:c.78del
  • NM_001368916.2:c.78del
  • NM_001368917.2:c.78del
  • NM_001368918.2:c.78del
  • NM_001368919.2:c.78del
  • NM_001368920.2:c.78del
  • NM_001368921.2:c.78del
  • NM_001368922.2:c.78del
  • NM_001368923.2:c.78del
  • NM_001368924.2:c.78del
  • NM_001368925.2:c.78del
  • NM_001368926.2:c.78del
  • NM_001368927.2:c.78del
  • NM_001368928.2:c.78del
  • NM_001368929.2:c.-373del
  • NM_001604.6:c.78del
  • NP_000271.1:p.Gln27fs
  • NP_001121084.1:p.Gln27fs
  • NP_001245391.1:p.Gln27fs
  • NP_001245392.1:p.Gln27fs
  • NP_001245393.1:p.Gln27fs
  • NP_001245394.1:p.Gln27fs
  • NP_001297087.1:p.Gln27fs
  • NP_001297088.1:p.Gln27fs
  • NP_001355816.1:p.Gln27fs
  • NP_001355817.1:p.Gln27fs
  • NP_001355818.1:p.Gln27fs
  • NP_001355819.1:p.Gln27fs
  • NP_001355820.1:p.Gln27fs
  • NP_001355821.1:p.Gln27fs
  • NP_001355822.1:p.Gln27fs
  • NP_001355823.1:p.Gln27fs
  • NP_001355839.1:p.Gln108fs
  • NP_001355840.1:p.Gln28fs
  • NP_001355841.1:p.Gln27fs
  • NP_001355842.1:p.Gln27fs
  • NP_001355843.1:p.Gln27fs
  • NP_001355844.1:p.Gln27fs
  • NP_001355845.1:p.Gln27fs
  • NP_001355846.1:p.Gln27fs
  • NP_001355847.1:p.Gln27fs
  • NP_001355848.1:p.Gln27fs
  • NP_001355849.1:p.Gln27fs
  • NP_001355850.1:p.Gln27fs
  • NP_001355851.1:p.Gln27fs
  • NP_001355852.1:p.Gln27fs
  • NP_001355853.1:p.Gln27fs
  • NP_001355854.1:p.Gln27fs
  • NP_001355855.1:p.Gln27fs
  • NP_001355856.1:p.Gln27fs
  • NP_001355857.1:p.Gln27fs
  • NP_001595.2:p.Gln27fs
  • LRG_720:g.20195del
  • NC_000011.9:g.31824315del
  • NC_000011.9:g.31824315delC
  • NC_000011.9:g.31824316del
  • NM_000280.4:c.78delG
  • NR_160916.2:n.500del
  • NR_160917.2:n.547del
Protein change:
Q108fs
Links:
dbSNP: rs1131692286
NCBI 1000 Genomes Browser:
rs1131692286
Molecular consequence:
  • NM_001310160.2:c.-704del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001310161.3:c.-373del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368899.2:c.-331del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368900.2:c.-373del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368901.2:c.-331del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368902.2:c.-662del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368903.2:c.-373del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368905.2:c.-704del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368906.2:c.-331del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368907.2:c.-331del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368908.2:c.-373del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001368929.2:c.-373del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000280.6:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127612.3:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001258462.3:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001258463.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001258464.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001258465.3:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001310158.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001310159.1:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368887.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368888.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368889.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368890.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368891.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368892.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368893.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368894.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368910.2:c.321del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368911.2:c.81del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368912.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368913.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368914.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368915.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368916.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368917.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368918.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368919.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368920.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368921.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368922.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368923.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368924.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368925.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368926.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368927.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368928.2:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001604.6:c.78del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001368904.2:c.-267-991del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001368909.2:c.-267-991del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_160916.2:n.500del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160917.2:n.547del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000944897Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 19, 2018) 		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

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

Molecular analysis of patients with aniridia in Russian Federation broadens the spectrum of PAX6 mutations.

Vasilyeva TA, Voskresenskaya AA, Käsmann-Kellner B, Khlebnikova OV, Pozdeyeva NA, Bayazutdinova GM, Kutsev SI, Ginter EK, Semina EV, Marakhonov AV, Zinchenko RA.

Clin Genet. 2017 Dec;92(6):639-644. doi: 10.1111/cge.13019. Epub 2017 Aug 2.

PubMed [citation]
PMID:
28321846
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000944897.4

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

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in PAX6 are known to be pathogenic (PMID: 12634864). A different variant (c.80delA) giving rise to the same protein effect observed here (p.Gln27Argfs*4) has been determined to be pathogenic (PMID: 10737978). This suggests that this variant is also likely to be causative of disease. This variant has been observed to be de novo in an individual affected with aniridia (PMID: 28321846). ClinVar contains an entry for this variant (Variation ID: 430974). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gln27Argfs*4) in the PAX6 gene. It is expected to 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