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NM_000278.5(PAX2):c.239C>T (p.Pro80Leu) AND multiple conditions

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Aug 27, 2021
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:
RCV000549890.7

Allele description [Variation Report for NM_000278.5(PAX2):c.239C>T (p.Pro80Leu)]

NM_000278.5(PAX2):c.239C>T (p.Pro80Leu)

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.239C>T (p.Pro80Leu)
HGVS:
  • NC_000010.11:g.100750720C>T
  • NG_008680.2:g.20012C>T
  • NM_000278.5:c.239C>TMANE SELECT
  • NM_001304569.2:c.332C>T
  • NM_003987.5:c.239C>T
  • NM_003988.5:c.239C>T
  • NM_003989.5:c.239C>T
  • NM_003990.5:c.239C>T
  • NP_000269.3:p.Pro80Leu
  • NP_001291498.1:p.Pro111Leu
  • NP_003978.3:p.Pro80Leu
  • NP_003979.2:p.Pro80Leu
  • NP_003980.3:p.Pro80Leu
  • NP_003981.3:p.Pro80Leu
  • NC_000010.10:g.102510477C>T
  • NM_003987.4:c.239C>T
  • NM_003988.3:c.239C>T
  • NM_003990.3:c.239C>T
Protein change:
P111L
Links:
dbSNP: rs1554856032
NCBI 1000 Genomes Browser:
rs1554856032
Molecular consequence:
  • NM_000278.5:c.239C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001304569.2:c.332C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003987.5:c.239C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003988.5:c.239C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003989.5:c.239C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003990.5:c.239C>T - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000641106Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 12, 2021) 		germlineclinical testing

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

SCV002811744Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Aug 27, 2021) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000641106.3

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

From Fulgent Genetics, Fulgent Genetics, SCV002811744.1

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

Last Updated: Oct 8, 2024