NM_016122.3(CEP83):c.1280A>G (p.Glu427Gly) AND Nephronophthisis 18

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 4, 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:: RCV001226617.4

Allele description

NM_016122.3(CEP83):c.1280A>G (p.Glu427Gly)

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.1280A>G (p.Glu427Gly)

HGVS:

NC_000012.12:g.94367857T>C
NG_051825.1:g.97132A>G
NM_001042399.2:c.1280A>G
NM_001346457.2:c.1280A>G
NM_001346458.2:c.968A>G
NM_001346459.2:c.968A>G
NM_001368037.1:c.1280A>G
NM_001368038.1:c.1280A>G
NM_001368039.1:c.968A>G
NM_001368040.1:c.968A>G
NM_001368041.1:c.1055A>G
NM_016122.3:c.1280A>GMANE SELECT
NP_001035858.1:p.Glu427Gly
NP_001333386.1:p.Glu427Gly
NP_001333387.1:p.Glu323Gly
NP_001333388.1:p.Glu323Gly
NP_001354966.1:p.Glu427Gly
NP_001354967.1:p.Glu427Gly
NP_001354968.1:p.Glu323Gly
NP_001354969.1:p.Glu323Gly
NP_001354970.1:p.Glu352Gly
NP_057206.2:p.Glu427Gly
NC_000012.11:g.94761633T>C
NM_016122.2:c.1280A>G
NR_160432.1:n.2033A>G

Protein change:

E323G

Links:

dbSNP: rs199501110

NCBI 1000 Genomes Browser:

rs199501110

Molecular consequence:

NM_001042399.2:c.1280A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346457.2:c.1280A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346458.2:c.968A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346459.2:c.968A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368037.1:c.1280A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368038.1:c.1280A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368039.1:c.968A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368040.1:c.968A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368041.1:c.1055A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_016122.3:c.1280A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_160432.1:n.2033A>G - 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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wol [Agrilus planipennis]
wol [Agrilus planipennis]
Gene ID:108733298

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PIGY [Gorilla gorilla gorilla]
PIGY [Gorilla gorilla gorilla]
Gene ID:109023057

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sfl [Agrilus planipennis]
sfl [Agrilus planipennis]
Gene ID:108735004

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001398938	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 4, 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

SCV001398938

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 4, 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 Invitae, SCV001398938.4

#	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 glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 427 of the CEP83 protein (p.Glu427Gly). This variant is present in population databases (rs199501110, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with CEP83-related conditions. ClinVar contains an entry for this variant (Variation ID: 954200). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on CEP83 protein function. 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: May 7, 2024

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