NM_025114.4(CEP290):c.4954G>T (p.Glu1652Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 31, 2023
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:: RCV003807043.2

Allele description [Variation Report for NM_025114.4(CEP290):c.4954G>T (p.Glu1652Ter)]

NM_025114.4(CEP290):c.4954G>T (p.Glu1652Ter)

Gene:

CEP290:centrosomal protein 290 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q21.32

Genomic location:

Preferred name:

NM_025114.4(CEP290):c.4954G>T (p.Glu1652Ter)

HGVS:

NC_000012.12:g.88083089C>A
NG_008417.2:g.64128G>T
NM_025114.4:c.4954G>TMANE SELECT
NP_079390.3:p.Glu1652Ter
LRG_694t1:c.4954G>T
LRG_694:g.64128G>T
LRG_694p1:p.Glu1652Ter
NC_000012.11:g.88476866C>A

Protein change:

E1652*

Molecular consequence:

NM_025114.4:c.4954G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Familial aplasia of the vermis
Synonyms:: CEREBELLOPARENCHYMAL DISORDER IV; Joubert syndrome; Cerebelloparenchymal disorder 4; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018772; MedGen: C0431399; Orphanet: 475; OMIM: PS213300

Name:: Meckel-Gruber syndrome
Synonyms:: DYSENCEPHALIA SPLANCHNOCYSTICA; Gruber syndrome; Dysencephalia splachnocystica
Identifiers:: MONDO: MONDO:0018921; MedGen: C0265215; OMIM: PS249000

Name:: Nephronophthisis
Synonyms:: juvenile nephronophthisis
Identifiers:: MONDO: MONDO:0019005; MedGen: C0687120; OMIM: PS256100; Human Phenotype Ontology: HP:0000090

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004594415	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 31, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 34821546, 16909394, 17345604, 20690115, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004594415

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 31, 2023)

germline

clinical testing

PubMed (5)
[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

Meckel Gruber and Joubert Syndrome Diagnosed Prenatally: Allelism between the Two Ciliopathies, Complexities of Mutation Types and Digenic Inheritance.

Srivastava S, Manisha R, Dwivedi A, Agarwal H, Saxena D, Agrawal V, Mandal K.

Fetal Pediatr Pathol. 2022 Dec;41(6):1041-1051. doi: 10.1080/15513815.2021.2007434. Epub 2021 Nov 25.

PubMed [citation]

PMID:: 34821546

Mutations in the CEP290 (NPHP6) gene are a frequent cause of Leber congenital amaurosis.

den Hollander AI, Koenekoop RK, Yzer S, Lopez I, Arends ML, Voesenek KE, Zonneveld MN, Strom TM, Meitinger T, Brunner HG, Hoyng CB, van den Born LI, Rohrschneider K, Cremers FP.

Am J Hum Genet. 2006 Sep;79(3):556-61. Epub 2006 Jul 11.

PubMed [citation]

PMID:: 16909394
PMCID:: PMC1559533

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004594415.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with Meckel syndrome (PMID: 34821546). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu1652*) in the CEP290 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CEP290 are known to be pathogenic (PMID: 16909394, 17345604, 20690115).

#	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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