NM_201548.5(CERKL):c.820+2C>A AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 15, 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:: RCV000806091.5

Allele description [Variation Report for NM_201548.5(CERKL):c.820+2C>A]

NM_201548.5(CERKL):c.820+2C>A

Gene:

CERKL:ceramide kinase like [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.3

Genomic location:

Preferred name:

NM_201548.5(CERKL):c.820+2C>A

HGVS:

NC_000002.12:g.181558564G>T
NG_021178.2:g.103544C>A
NM_001030311.3:c.898+2C>A
NM_001030312.3:c.482-8856C>A
NM_001030313.3:c.614-8856C>A
NM_001160277.2:c.766+2C>A
NM_201548.5:c.820+2C>AMANE SELECT
NC_000002.11:g.182423291G>T
NM_001030311.2:c.898+2C>A

Links:

dbSNP: rs1328971667

NCBI 1000 Genomes Browser:

rs1328971667

Molecular consequence:

NM_001030312.3:c.482-8856C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001030313.3:c.614-8856C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001030311.3:c.898+2C>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001160277.2:c.766+2C>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_201548.5:c.820+2C>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000946072	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 15, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16199547, 14681825, 23591405, 24043777, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000946072

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 15, 2022)

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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Mutation of CERKL, a novel human ceramide kinase gene, causes autosomal recessive retinitis pigmentosa (RP26).

Tuson M, Marfany G, Gonzàlez-Duarte R.

Am J Hum Genet. 2004 Jan;74(1):128-38. Epub 2003 Dec 16.

PubMed [citation]

PMID:: 14681825
PMCID:: PMC1181900

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000946072.4

#	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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 650853). Disruption of this splice site has been observed in individuals with clinical features of inherited retinal dystrophy (Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 6 of the CERKL gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CERKL are known to be pathogenic (PMID: 14681825, 23591405, 24043777).

#	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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