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NM_001368894.2(PAX6):c.1310A>T (p.Ter437Leu) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:
Jan 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000327291.27

Allele description [Variation Report for NM_001368894.2(PAX6):c.1310A>T (p.Ter437Leu)]

NM_001368894.2(PAX6):c.1310A>T (p.Ter437Leu)

Genes:
ELP4:elongator acetyltransferase complex subunit 4 [Gene - OMIM - HGNC]
PAX6:paired box 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p13
Genomic location:
Preferred name:
NM_001368894.2(PAX6):c.1310A>T (p.Ter437Leu)
Other names:
*423L; *437L; *462L; *287L; *222L; *356L; *370L; *448L; *504L
HGVS:
  • NC_000011.10:g.31789935T>A
  • NG_008679.1:g.33027A>T
  • NM_000280.6:c.1268A>T
  • NM_001127612.3:c.1268A>T
  • NM_001258462.3:c.1310A>T
  • NM_001258463.2:c.1310A>T
  • NM_001258464.2:c.1268A>T
  • NM_001258465.3:c.1268A>T
  • NM_001288725.2:c.*6397T>A
  • NM_001288726.2:c.*6506T>A
  • NM_001310158.2:c.1310A>T
  • NM_001310160.2:c.860A>T
  • NM_001310161.3:c.860A>T
  • NM_001368887.2:c.1268A>T
  • NM_001368888.2:c.1268A>T
  • NM_001368889.2:c.1268A>T
  • NM_001368890.2:c.1268A>T
  • NM_001368891.2:c.1268A>T
  • NM_001368892.2:c.1310A>T
  • NM_001368893.2:c.1310A>T
  • NM_001368894.2:c.1310A>TMANE SELECT
  • NM_001368899.2:c.860A>T
  • NM_001368900.2:c.860A>T
  • NM_001368901.2:c.860A>T
  • NM_001368902.2:c.860A>T
  • NM_001368903.2:c.860A>T
  • NM_001368904.2:c.860A>T
  • NM_001368905.2:c.860A>T
  • NM_001368906.2:c.860A>T
  • NM_001368907.2:c.860A>T
  • NM_001368908.2:c.860A>T
  • NM_001368909.2:c.860A>T
  • NM_001368910.2:c.1511A>T
  • NM_001368911.2:c.1162A>T
  • NM_001368912.2:c.1159A>T
  • NM_001368913.2:c.1159A>T
  • NM_001368914.2:c.1159A>T
  • NM_001368915.2:c.1117A>T
  • NM_001368916.2:c.1117A>T
  • NM_001368917.2:c.1117A>T
  • NM_001368918.2:c.1385A>T
  • NM_001368919.2:c.1385A>T
  • NM_001368920.2:c.1343A>T
  • NM_001368921.2:c.958A>T
  • NM_001368922.2:c.1109A>T
  • NM_001368923.2:c.1109A>T
  • NM_001368924.2:c.1109A>T
  • NM_001368925.2:c.1109A>T
  • NM_001368926.2:c.1109A>T
  • NM_001368927.2:c.1109A>T
  • NM_001368928.2:c.1067A>T
  • NM_001368929.2:c.709A>T
  • NM_001368930.2:c.665A>T
  • NM_001604.6:c.1310A>T
  • NM_019040.5:c.*6411T>AMANE SELECT
  • NP_000271.1:p.Ter423Leu
  • NP_000271.1:p.Ter423Leu
  • NP_001121084.1:p.Ter423Leu
  • NP_001245391.1:p.Ter437Leu
  • NP_001245392.1:p.Ter437Leu
  • NP_001245393.1:p.Ter423Leu
  • NP_001245394.1:p.Ter423Leu
  • NP_001297087.1:p.Ter437Leu
  • NP_001297089.1:p.Ter287Leu
  • NP_001297090.1:p.Ter287Leu
  • NP_001355816.1:p.Ter423Leu
  • NP_001355817.1:p.Ter423Leu
  • NP_001355818.1:p.Ter423Leu
  • NP_001355819.1:p.Ter423Leu
  • NP_001355820.1:p.Ter423Leu
  • NP_001355821.1:p.Ter437Leu
  • NP_001355822.1:p.Ter437Leu
  • NP_001355823.1:p.Ter437Leu
  • NP_001355828.1:p.Ter287Leu
  • NP_001355829.1:p.Ter287Leu
  • NP_001355830.1:p.Ter287Leu
  • NP_001355831.1:p.Ter287Leu
  • NP_001355832.1:p.Ter287Leu
  • NP_001355833.1:p.Ter287Leu
  • NP_001355834.1:p.Ter287Leu
  • NP_001355835.1:p.Ter287Leu
  • NP_001355836.1:p.Ter287Leu
  • NP_001355837.1:p.Ter287Leu
  • NP_001355838.1:p.Ter287Leu
  • NP_001355839.1:p.Ter504Leu
  • NP_001355840.1:p.Lys388Ter
  • NP_001355841.1:p.Lys387Ter
  • NP_001355842.1:p.Lys387Ter
  • NP_001355843.1:p.Lys387Ter
  • NP_001355844.1:p.Lys373Ter
  • NP_001355845.1:p.Lys373Ter
  • NP_001355846.1:p.Lys373Ter
  • NP_001355847.1:p.Ter462Leu
  • NP_001355848.1:p.Ter462Leu
  • NP_001355849.1:p.Ter448Leu
  • NP_001355850.1:p.Lys320Ter
  • NP_001355851.1:p.Ter370Leu
  • NP_001355852.1:p.Ter370Leu
  • NP_001355853.1:p.Ter370Leu
  • NP_001355854.1:p.Ter370Leu
  • NP_001355855.1:p.Ter370Leu
  • NP_001355856.1:p.Ter370Leu
  • NP_001355857.1:p.Ter356Leu
  • NP_001355858.1:p.Lys237Ter
  • NP_001355859.1:p.Ter222Leu
  • NP_001595.2:p.Ter437Leu
  • NP_001595.2:p.Ter437Leu
  • LRG_720t1:c.1268A>T
  • LRG_720:g.33027A>T
  • NC_000011.9:g.31811483T>A
  • NM_000280.3:c.1268A>T
  • NM_000280.4:c.1268A>T
  • NM_001604.5:c.1310A>T
  • NR_160916.2:n.1498A>T
  • NR_160917.2:n.1654A>T
  • p.(Ter423LeuextTer14)
Protein change:
K237*; TER423LEU
Links:
OMIM: 607108.0016; dbSNP: rs121907922
NCBI 1000 Genomes Browser:
rs121907922
Molecular consequence:
  • NM_001288725.2:c.*6397T>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001288726.2:c.*6506T>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_019040.5:c.*6411T>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NR_160916.2:n.1498A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160917.2:n.1654A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001368911.2:c.1162A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001368912.2:c.1159A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001368913.2:c.1159A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001368914.2:c.1159A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001368915.2:c.1117A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001368916.2:c.1117A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001368917.2:c.1117A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001368921.2:c.958A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001368929.2:c.709A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000280.6:c.1268A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001127612.3:c.1268A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001258462.3:c.1310A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001258463.2:c.1310A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001258464.2:c.1268A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001258465.3:c.1268A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001310158.2:c.1310A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001310160.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001310161.3:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368887.2:c.1268A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368888.2:c.1268A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368889.2:c.1268A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368890.2:c.1268A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368891.2:c.1268A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368892.2:c.1310A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368893.2:c.1310A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368894.2:c.1310A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368899.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368900.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368901.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368902.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368903.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368904.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368905.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368906.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368907.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368908.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368909.2:c.860A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368910.2:c.1511A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368918.2:c.1385A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368919.2:c.1385A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368920.2:c.1343A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368922.2:c.1109A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368923.2:c.1109A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368924.2:c.1109A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368925.2:c.1109A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368926.2:c.1109A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368927.2:c.1109A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368928.2:c.1067A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001368930.2:c.665A>T - stop lost - [Sequence Ontology: SO:0001578]
  • NM_001604.6:c.1310A>T - stop lost - [Sequence Ontology: SO:0001578]
Observations:
4

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000225770Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Pathogenic
(Jan 15, 2015) 		germlineclinical testing

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

Citation Link,

SCV000329453GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Dec 27, 2021) 		germlineclinical testing

Citation Link,

SCV001247619CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Pathogenic
(Jan 1, 2024) 		germlineclinical testing

Citation Link,

SCV001450012Clinical Genetics and Genomics, Karolinska University Hospital
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Mar 15, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes3not providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

PAX6 haploinsufficiency causes cerebral malformation and olfactory dysfunction in humans.

Sisodiya SM, Free SL, Williamson KA, Mitchell TN, Willis C, Stevens JM, Kendall BE, Shorvon SD, Hanson IM, Moore AT, van Heyningen V.

Nat Genet. 2001 Jul;28(3):214-6.

PubMed [citation]
PMID:
11431688

Polymicrogyria and absence of pineal gland due to PAX6 mutation.

Mitchell TN, Free SL, Williamson KA, Stevens JM, Churchill AJ, Hanson IM, Shorvon SD, Moore AT, van Heyningen V, Sisodiya SM.

Ann Neurol. 2003 May;53(5):658-63.

PubMed [citation]
PMID:
12731001
See all PubMed Citations (4)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000225770.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000329453.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Normal stop codon changed to a Leucine codon, leading to the addition of 14 amino acids at the C-terminus; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 18494745, 20132240, 28321846, 21850189, 25555363, 22204637, 16098226, 6330922, 18494744, 16199712, 22361317, 28698011, 18241071, 10477494, 11309364, 26661695, 12552561, 27431685, 29618921, 29367200, 32360764, 33594928, 27535533, 34101622, 33726816, 32467297)

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

From CeGaT Center for Human Genetics Tuebingen, SCV001247619.22

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

PAX6: PP1:Strong, PM2, PM4, PS4:Moderate, PM6:Supporting, PP4

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From Clinical Genetics and Genomics, Karolinska University Hospital, SCV001450012.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 17, 2024