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NM_016122.3(CEP83):c.428A>C (p.Lys143Thr) AND Nephronophthisis 18

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 13, 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:
RCV002895910.3

Allele description [Variation Report for NM_016122.3(CEP83):c.428A>C (p.Lys143Thr)]

NM_016122.3(CEP83):c.428A>C (p.Lys143Thr)

Gene:
CEP83:centrosomal protein 83 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q22
Genomic location:
Preferred name:
NM_016122.3(CEP83):c.428A>C (p.Lys143Thr)
HGVS:
  • NC_000012.12:g.94400971T>G
  • NG_051825.1:g.64018A>C
  • NG_051825.2:g.64483A>C
  • NM_001042399.2:c.428A>C
  • NM_001346457.2:c.428A>C
  • NM_001346458.2:c.116A>C
  • NM_001346459.2:c.116A>C
  • NM_001346460.2:c.428A>C
  • NM_001346461.2:c.428A>C
  • NM_001346462.2:c.116A>C
  • NM_001368037.1:c.428A>C
  • NM_001368038.1:c.428A>C
  • NM_001368039.1:c.116A>C
  • NM_001368040.1:c.116A>C
  • NM_001368041.1:c.324+10726A>C
  • NM_001368042.1:c.12+10726A>C
  • NM_016122.3:c.428A>CMANE SELECT
  • NP_001035858.1:p.Lys143Thr
  • NP_001333386.1:p.Lys143Thr
  • NP_001333387.1:p.Lys39Thr
  • NP_001333388.1:p.Lys39Thr
  • NP_001333389.1:p.Lys143Thr
  • NP_001333390.1:p.Lys143Thr
  • NP_001333391.1:p.Lys39Thr
  • NP_001354966.1:p.Lys143Thr
  • NP_001354967.1:p.Lys143Thr
  • NP_001354968.1:p.Lys39Thr
  • NP_001354969.1:p.Lys39Thr
  • NP_057206.2:p.Lys143Thr
  • NC_000012.11:g.94794747T>G
  • NR_144441.2:n.778A>C
  • NR_160431.1:n.694A>C
  • NR_160432.1:n.1181A>C
Protein change:
K143T
Molecular consequence:
  • NM_001368041.1:c.324+10726A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001368042.1:c.12+10726A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001042399.2:c.428A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346457.2:c.428A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346458.2:c.116A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346459.2:c.116A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346460.2:c.428A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346461.2:c.428A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001346462.2:c.116A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368037.1:c.428A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368038.1:c.428A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368039.1:c.116A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368040.1:c.116A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_016122.3:c.428A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_144441.2:n.778A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160431.1:n.694A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_160432.1:n.1181A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Nephronophthisis 18 (NPHP18)
Identifiers:
MONDO: MONDO:0014374; MedGen: C3890591; Orphanet: 655; OMIM: 615862

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003250284Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 13, 2022) 		germlineclinical 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

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003250284.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with CEP83-related conditions. 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CEP83 protein function. This variant is present in population databases (no rsID available, gnomAD 0.008%). This sequence change replaces lysine, which is basic and polar, with threonine, which is neutral and polar, at codon 143 of the CEP83 protein (p.Lys143Thr).

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

Last Updated: Sep 29, 2024