NM_000325.6(PITX2):c.411+1G>A AND Axenfeld-Rieger syndrome type 1

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 23, 2022
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:: RCV001090057.6

Allele description [Variation Report for NM_000325.6(PITX2):c.411+1G>A]

NM_000325.6(PITX2):c.411+1G>A

Gene:

PITX2:paired like homeodomain 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q25

Genomic location:

Preferred name:

NM_000325.6(PITX2):c.411+1G>A

HGVS:

NC_000004.12:g.110621163C>T
NG_007120.1:g.21190G>A
NG_103304.1:g.231C>T
NM_000325.6:c.411+1G>AMANE SELECT
NM_001204397.2:c.390+1G>A
NM_001204398.1:c.390+1G>A
NM_001204399.1:c.252+1G>A
NM_153426.3:c.390+1G>A
NM_153427.3:c.252+1G>A
NC_000004.11:g.111542319C>T
NM_001204397.1:c.390+1G>A
NM_153427.2:c.252+1G>A

Links:

dbSNP: rs1728998905

NCBI 1000 Genomes Browser:

rs1728998905

Molecular consequence:

NM_000325.6:c.411+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001204397.2:c.390+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001204398.1:c.390+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001204399.1:c.252+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_153426.3:c.390+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_153427.3:c.252+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Functional consequence:

sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071]

Condition(s)

Name:: Axenfeld-Rieger syndrome type 1 (RIEG1)
Synonyms:: Rieger syndrome type 1
Identifiers:: MONDO: MONDO:0008386; MedGen: C3714873; Orphanet: 782; OMIM: 180500

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PREDICTED: Perca flavescens NKD inhibitor of WNT signaling pathway 1 (nkd1), mRN...
PREDICTED: Perca flavescens NKD inhibitor of WNT signaling pathway 1 (nkd1), mRNA
gi|1604763646|ref|XM_028578708.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000998747	Hunan Clinical Research Center of Ophthalmic Disease, The Second Xiangya Hospital	criteria provided, single submitter (Zhang et al. (Int Ophthalmol. 2021))	Pathogenic	inherited	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002538928	Human Developmental Genetics Laboratory, Medical College of Wisconsin	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 23, 2022)	germline	research	PubMed (2) [See all records that cite these PMIDs] 25741868, 35882526

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000998747

Hunan Clinical Research Center of Ophthalmic Disease, The Second Xiangya Hospital

criteria provided, single submitter

(Zhang et al. (Int Ophthalmol. 2021))

Pathogenic

inherited

clinical testing

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

SCV002538928

Human Developmental Genetics Laboratory, Medical College of Wisconsin

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 23, 2022)

germline

research

PubMed (2)
[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	yes	1	not provided	not provided	not provided	not provided	research
Chinese	inherited	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A PITX2 splice-site mutation in a family with Axenfeld-Rieger syndrome leads to decreased expression of nuclear PITX2 protein.

Zhang F, Zhang L, He L, Cao M, Yang Y, Duan X, Shi J, Liu K.

Int Ophthalmol. 2021 Apr;41(4):1503-1511. doi: 10.1007/s10792-021-01704-5. Epub 2021 Jan 25.

PubMed [citation]

PMID:: 33492563
PMCID:: PMC8035109

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

See all PubMed Citations (3)

Details of each submission

From Hunan Clinical Research Center of Ophthalmic Disease, The Second Xiangya Hospital, SCV000998747.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Chinese	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	inherited	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Human Developmental Genetics Laboratory, Medical College of Wisconsin, SCV002538928.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	research	PubMed (2)

#	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		1	not provided	not provided	not provided

Last Updated: Nov 11, 2023

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