NM_016122.3(CEP83):c.1655A>T (p.Lys552Met) AND Nephronophthisis 18

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 23, 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:: RCV001924740.5

Allele description [Variation Report for NM_016122.3(CEP83):c.1655A>T (p.Lys552Met)]

NM_016122.3(CEP83):c.1655A>T (p.Lys552Met)

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.1655A>T (p.Lys552Met)

HGVS:

NC_000012.12:g.94331752T>A
NG_051825.1:g.133237A>T
NM_001042399.2:c.1655A>T
NM_001346457.2:c.1655A>T
NM_001346458.2:c.1343A>T
NM_001346459.2:c.1343A>T
NM_001368037.1:c.1655A>T
NM_001368038.1:c.1655A>T
NM_001368039.1:c.1343A>T
NM_001368040.1:c.1343A>T
NM_001368041.1:c.1430A>T
NM_016122.3:c.1655A>TMANE SELECT
NP_001035858.1:p.Lys552Met
NP_001333386.1:p.Lys552Met
NP_001333387.1:p.Lys448Met
NP_001333388.1:p.Lys448Met
NP_001354966.1:p.Lys552Met
NP_001354967.1:p.Lys552Met
NP_001354968.1:p.Lys448Met
NP_001354969.1:p.Lys448Met
NP_001354970.1:p.Lys477Met
NP_057206.2:p.Lys552Met
NC_000012.11:g.94725528T>A
NR_160431.1:n.1379A>T
NR_160432.1:n.2400A>T

Protein change:

K448M

Links:

dbSNP: rs377015196

NCBI 1000 Genomes Browser:

rs377015196

Molecular consequence:

NM_001042399.2:c.1655A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001346457.2:c.1655A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001346458.2:c.1343A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001346459.2:c.1343A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368037.1:c.1655A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368038.1:c.1655A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368039.1:c.1343A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368040.1:c.1343A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368041.1:c.1430A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_016122.3:c.1655A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_160431.1:n.1379A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_160432.1:n.2400A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

Recent activity

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Homo sapiens enolase 1 (ENO1), transcript variant 3, mRNA
Homo sapiens enolase 1 (ENO1), transcript variant 3, mRNA
gi|1674986104|ref|NM_001353346.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002153691	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 23, 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

SCV002153691

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 23, 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

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, SCV002153691.2

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

Description

This sequence change replaces lysine, which is basic and polar, with methionine, which is neutral and non-polar, at codon 552 of the CEP83 protein (p.Lys552Met). This variant is present in population databases (rs377015196, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with CEP83-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). 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.

#	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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