NM_201548.5(CERKL):c.2T>G (p.Met1Arg) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 14, 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:: RCV000797385.5

Allele description [Variation Report for NM_201548.5(CERKL):c.2T>G (p.Met1Arg)]

NM_201548.5(CERKL):c.2T>G (p.Met1Arg)

Genes:

LOC129935215:ATAC-STARR-seq lymphoblastoid silent region 12158 [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.2T>G (p.Met1Arg)

HGVS:

NC_000002.12:g.181657005A>C
NG_021178.2:g.5103T>G
NM_001030311.3:c.2T>G
NM_001030312.3:c.2T>G
NM_001030313.3:c.2T>G
NM_001160277.2:c.2T>G
NM_201548.5:c.2T>GMANE SELECT
NP_001025482.1:p.Met1Arg
NP_001025482.1:p.Met1Arg
NP_001025483.1:p.Met1Arg
NP_001025484.1:p.Met1Arg
NP_001153749.1:p.Met1Arg
NP_963842.1:p.Met1Arg
NC_000002.11:g.182521732A>C
NM_001030311.2:c.2T>G
NR_027689.2:n.101T>G
NR_027690.2:n.101T>G

Protein change:

M1R

Links:

dbSNP: rs1187991259

NCBI 1000 Genomes Browser:

rs1187991259

Molecular consequence:

NM_001030311.3:c.2T>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001030312.3:c.2T>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001030313.3:c.2T>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001160277.2:c.2T>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_201548.5:c.2T>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001030311.3:c.2T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001030312.3:c.2T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001030313.3:c.2T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160277.2:c.2T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_201548.5:c.2T>G - missense variant - [Sequence Ontology: SO:0001583]
NR_027689.2:n.101T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_027690.2:n.101T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000936939	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 14, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 20554613, 24498393, 29068140, 31456290, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000936939

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 14, 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

Homozygosity mapping in patients with cone-rod dystrophy: novel mutations and clinical characterizations.

Littink KW, Koenekoop RK, van den Born LI, Collin RW, Moruz L, Veltman JA, Roosing S, Zonneveld MN, Omar A, Darvish M, Lopez I, Kroes HY, van Genderen MM, Hoyng CB, Rohrschneider K, van Schooneveld MJ, Cremers FP, den Hollander AI.

Invest Ophthalmol Vis Sci. 2010 Nov;51(11):5943-51. doi: 10.1167/iovs.10-5797. Epub 2010 Jun 16.

PubMed [citation]

PMID:: 20554613
PMCID:: PMC3061516

CERKL, a retinal disease gene, encodes an mRNA-binding protein that localizes in compact and untranslated mRNPs associated with microtubules.

Fathinajafabadi A, Pérez-Jiménez E, Riera M, Knecht E, Gonzàlez-Duarte R.

PLoS One. 2014;9(2):e87898. doi: 10.1371/journal.pone.0087898.

PubMed [citation]

PMID:: 24498393
PMCID:: PMC3912138

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000936939.5

#	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 variant disrupts a region of the CERKL protein in which other variant(s) (p.Cys125Trp) have been determined to be pathogenic (PMID: 20554613, 24498393, 29068140). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 643636). Disruption of the initiator codon has been observed in individual(s) with clinical features of retinitis pigmentosa (PMID: 31456290; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change affects the initiator methionine of the CERKL mRNA. The next in-frame methionine is located at codon 206.

#	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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