NM_000278.5(PAX2):c.491C>G (p.Thr164Ser) AND PAX2-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 22, 2022
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:: RCV004538970.1

Allele description [Variation Report for NM_000278.5(PAX2):c.491C>G (p.Thr164Ser)]

NM_000278.5(PAX2):c.491C>G (p.Thr164Ser)

Gene:

PAX2:paired box 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q24.31

Genomic location:

Preferred name:

NM_000278.5(PAX2):c.491C>G (p.Thr164Ser)

HGVS:

NC_000010.11:g.100779578C>G
NG_008680.2:g.48870C>G
NM_000278.5:c.491C>GMANE SELECT
NM_001304569.2:c.584C>G
NM_003987.5:c.491C>G
NM_003988.5:c.491C>G
NM_003989.5:c.491C>G
NM_003990.5:c.491C>G
NP_000269.3:p.Thr164Ser
NP_001291498.1:p.Thr195Ser
NP_003978.3:p.Thr164Ser
NP_003979.2:p.Thr164Ser
NP_003980.3:p.Thr164Ser
NP_003981.3:p.Thr164Ser
NC_000010.10:g.102539335C>G
NM_003990.4:c.491C>G

Protein change:

T164S

Molecular consequence:

NM_000278.5:c.491C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001304569.2:c.584C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003987.5:c.491C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003988.5:c.491C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003989.5:c.491C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003990.5:c.491C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: PAX2-related disorder
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004106759	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 22, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004106759

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 22, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004106759.1

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

Description

The PAX2 c.491C>G variant is predicted to result in the amino acid substitution p.Thr164Ser. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. A different substitution at this amino acid position (p.Thr164Asn) has been reported to be pathogenic for PAX2-related disorders in two individuals (Barua. 2014. PubMed ID: 24676634; Connaughton. 2019. PubMed ID: 30773290). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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

Last Updated: Nov 10, 2024

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