NM_004859.4(CLTC):c.3065+1G>A AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 17, 2017
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:: RCV000579309.1

Allele description [Variation Report for NM_004859.4(CLTC):c.3065+1G>A]

NM_004859.4(CLTC):c.3065+1G>A

Gene:

CLTC:clathrin heavy chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q23.1

Genomic location:

Preferred name:

NM_004859.4(CLTC):c.3065+1G>A

HGVS:

NC_000017.11:g.59681058G>A
NG_047043.1:g.66370G>A
NM_001288653.2:c.3077+1G>A
NM_004859.4:c.3065+1G>AMANE SELECT
NC_000017.10:g.57758419G>A
NM_001288653.1:c.3077+1G>A

Links:

dbSNP: rs750846632

NCBI 1000 Genomes Browser:

rs750846632

Molecular consequence:

NM_001288653.2:c.3077+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_004859.4:c.3065+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000681016	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Nov 17, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000681016

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Nov 17, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000681016.2

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

Description

The c.3077+1G>A variant in the CLTC gene has not been reported previously as a pathogenic variantnor as a benign variant, to our knowledge. This splice site variant destroys the canonical splice donorsite in intron 19. It is predicted to cause abnormal gene splicing, either leading to an abnormal messagethat is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message isused for protein translation. The c.3077+1G>A variant is not observed in large population cohorts(Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpretc.3077+1G>A as a likely pathogenic variant.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 10, 2023

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