NM_000278.5(PAX2):c.194T>C (p.Val65Ala) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 7, 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:: RCV003019241.3

Allele description [Variation Report for NM_000278.5(PAX2):c.194T>C (p.Val65Ala)]

NM_000278.5(PAX2):c.194T>C (p.Val65Ala)

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.194T>C (p.Val65Ala)

HGVS:

NC_000010.11:g.100749896T>C
NG_008680.2:g.19188T>C
NM_000278.5:c.194T>CMANE SELECT
NM_001304569.2:c.287T>C
NM_003987.5:c.194T>C
NM_003988.5:c.194T>C
NM_003989.5:c.194T>C
NM_003990.5:c.194T>C
NP_000269.3:p.Val65Ala
NP_001291498.1:p.Val96Ala
NP_003978.3:p.Val65Ala
NP_003979.2:p.Val65Ala
NP_003980.3:p.Val65Ala
NP_003981.3:p.Val65Ala
NC_000010.10:g.102509653T>C

Protein change:

V65A

Molecular consequence:

NM_000278.5:c.194T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001304569.2:c.287T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003987.5:c.194T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003988.5:c.194T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003989.5:c.194T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003990.5:c.194T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Renal coloboma syndrome (PAPRS)
Synonyms:: RENAL-COLOBOMA SYNDROME WITH MACULAR ABNORMALITIES; Papillorenal syndrome; Optic nerve coloboma with renal disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007352; MedGen: C1852759; Orphanet: 1475; OMIM: 120330

Name:: Focal segmental glomerulosclerosis 7 (FSGS7)
Identifiers:: MONDO: MONDO:0014451; MedGen: C4014925; Orphanet: 656; OMIM: 616002

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003314166	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 7, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34031707, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003314166

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 7, 2022)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Diagnostic and clinical utility of genetic testing in children with kidney failure.

Chen J, Lin F, Zhai Y, Wang C, Wu B, Ma D, Rao J, Liu J, Liu J, Yu M, Shen Q, Xu H.

Pediatr Nephrol. 2021 Nov;36(11):3653-3662. doi: 10.1007/s00467-021-05141-5. Epub 2021 May 24.

PubMed [citation]

PMID:: 34031707

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003314166.2

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

Description

This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 65 of the PAX2 protein (p.Val65Ala). This variant is not present in population databases (gnomAD no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This missense change has been observed in individual(s) with PAX2-related conditions (PMID: 34031707).

#	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: Sep 29, 2024

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