NM_015335.5(MED13L):c.5978G>A (p.Cys1993Tyr) AND Cardiac anomalies - developmental delay - facial dysmorphism syndrome - ClinVar

NM_015335.5(MED13L):c.5978G>A (p.Cys1993Tyr) AND Cardiac anomalies - developmental delay - facial dysmorphism syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 25, 2021
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:: RCV001779384.1

Allele description [Variation Report for NM_015335.5(MED13L):c.5978G>A (p.Cys1993Tyr)]

NM_015335.5(MED13L):c.5978G>A (p.Cys1993Tyr)

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.5978G>A (p.Cys1993Tyr)

HGVS:

NC_000012.12:g.115970683C>T
NG_023366.1:g.311504G>A
NM_015335.5:c.5978G>AMANE SELECT
NP_056150.1:p.Cys1993Tyr
NC_000012.11:g.116408488C>T
NM_015335.4:c.5978G>A

Protein change:

C1993Y

Links:

dbSNP: rs2137223521

NCBI 1000 Genomes Browser:

rs2137223521

Molecular consequence:

NM_015335.5:c.5978G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002014723	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 25, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002014723

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 25, 2021)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	1	not provided	not provided	1	not provided	clinical testing

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

Details of each submission

From 3billion, SCV002014723.1

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

Description

This varant is not observed in the gnomAD v2.1.1 dataset (PM2). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.859, PP3). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Feb 4, 2024

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