NM_015335.5(MED13L):c.5588+1G>A AND Cardiac anomalies - developmental delay - facial dysmorphism syndrome - ClinVar

NM_015335.5(MED13L):c.5588+1G>A AND Cardiac anomalies - developmental delay - facial dysmorphism syndrome

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 6, 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:: RCV000496142.3

Allele description [Variation Report for NM_015335.5(MED13L):c.5588+1G>A]

NM_015335.5(MED13L):c.5588+1G>A

Gene:

MED13L:mediator complex subunit 13L [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q24.21

Genomic location:

Preferred name:

NM_015335.5(MED13L):c.5588+1G>A

HGVS:

NC_000012.12:g.115975514C>T
NG_023366.1:g.306673G>A
NM_015335.5:c.5588+1G>AMANE SELECT
NC_000012.11:g.116413319C>T
NM_015335.4:c.5588+1G>A

Links:

dbSNP: rs1135401810

NCBI 1000 Genomes Browser:

rs1135401810

Molecular consequence:

NM_015335.5:c.5588+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Observations:

Condition(s)

Name:: Cardiac anomalies - developmental delay - facial dysmorphism syndrome (MRFACD)
Identifiers:: MONDO: MONDO:0014773; MedGen: C4225208; Orphanet: 369891; OMIM: 616789

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000586777	Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 6, 2017)	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 28708303
SCV001443162	GenomeConnect - Simons Searchlight	no assertion criteria provided	Likely pathogenic (Feb 21, 2017)	inherited	provider interpretation

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000586777

Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 6, 2017)

de novo

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001443162

GenomeConnect - Simons Searchlight

no assertion criteria provided

Likely pathogenic
(Feb 21, 2017)

inherited

provider interpretation

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	2	not provided	not provided	not provided	not provided	clinical testing
not provided	inherited	yes	not provided	not provided	not provided	not provided	not provided	provider interpretation

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Using medical exome sequencing to identify the causes of neurodevelopmental disorders: Experience of 2 clinical units and 216 patients.

Chérot E, Keren B, Dubourg C, Carré W, Fradin M, Lavillaureix A, Afenjar A, Burglen L, Whalen S, Charles P, Marey I, Heide S, Jacquette A, Heron D, Doummar D, Rodriguez D, Billette de Villemeur T, Moutard ML, Guët A, Xavier J, Périsse D, Cohen D, et al.

Clin Genet. 2018 Mar;93(3):567-576. doi: 10.1111/cge.13102. Epub 2017 Oct 4.

PubMed [citation]

PMID:: 28708303

Details of each submission

From Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris, SCV000586777.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (2)

Description

Intellectual disability, moderate; pyramidal syndrome; overweight

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		2	not provided	not provided	not provided

From GenomeConnect - Simons Searchlight, SCV001443162.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	provider interpretation	not provided

Description

Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2017-02-21 and interpreted as Likely Pathogenic. Variant was initially reported on 2016-03-02 by GTR ID of laboratory name Hopitaux Universitaires Pitie-Salpetriere Charles Foix . The reporting laboratory might also submit to ClinVar. Identified in multiple siblings and inherited from a parent with germline mosaicism. Additional phenotypic information for other sibling(s) might be available from Simons Searchlight.

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

Last Updated: Feb 4, 2024

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