NM_003482.4(KMT2D):c.15902_15903del (p.Val5301fs) AND Kabuki syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 1, 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:: RCV000680025.2

Allele description [Variation Report for NM_003482.4(KMT2D):c.15902_15903del (p.Val5301fs)]

NM_003482.4(KMT2D):c.15902_15903del (p.Val5301fs)

Gene:

KMT2D:lysine methyltransferase 2D [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q13.12

Genomic location:

Preferred name:

NM_003482.4(KMT2D):c.15902_15903del (p.Val5301fs)

HGVS:

NC_000012.12:g.49024829_49024830del
NG_027827.1:g.35496_35497del
NM_003482.4:c.15902_15903delMANE SELECT
NP_003473.3:p.Val5301fs
NP_003473.3:p.Val5301fs
NC_000012.11:g.49418612_49418613del
NM_003482.3:c.15902_15903del

Protein change:

V5301fs

Links:

dbSNP: rs1565756561

NCBI 1000 Genomes Browser:

rs1565756561

Molecular consequence:

NM_003482.4:c.15902_15903del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Kabuki syndrome 1 (KABUK1)
Identifiers:: MONDO: MONDO:0007843; MedGen: CN030661; Orphanet: 2322; OMIM: 147920

Recent activity

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Mus musculus G protein-coupled receptor 153 (Gpr153), transcript variant 1, mRNA
Mus musculus G protein-coupled receptor 153 (Gpr153), transcript variant 1, mRNA
gi|118130589|ref|NM_178406.2|

Nucleotide
Fam131c family with sequence similarity 131, member C [Mus musculus]
Fam131c family with sequence similarity 131, member C [Mus musculus]
Gene ID:277743

Gene
277743[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000807464	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 1, 2017)	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 25326635

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000807464

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 1, 2017)

de novo

clinical testing

PubMed (2)
[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	de novo	yes	not provided	not provided	not provided	not provided	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

Molecular findings among patients referred for clinical whole-exome sequencing.

Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen WJ, Bekheirnia MR, et al.

JAMA. 2014 Nov 12;312(18):1870-9. doi: 10.1001/jama.2014.14601.

PubMed [citation]

PMID:: 25326635
PMCID:: PMC4326249

Details of each submission

From Baylor Genetics, SCV000807464.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing (GTR000508680.4)	PubMed (2)

Description

This frameshift mutation is categorized as deleterious according to ACMG guidelines (PMID:18414213) and was found once in our laboratory de novo in a 1-year-old male with global delays, hypotonia, hearing loss, abnormal movements, dysmorphisms, microretrognathia, VSD, horseshoe kidney, broad thumbs

#	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	(GTR000508680.4)	not provided	not provided	not provided	not provided

Last Updated: Dec 11, 2022

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