NM_017635.5(KMT5B):c.268G>A (p.Asp90Asn) AND Intellectual disability, autosomal dominant 51

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 18, 2020
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:: RCV001837412.1

Allele description [Variation Report for NM_017635.5(KMT5B):c.268G>A (p.Asp90Asn)]

NM_017635.5(KMT5B):c.268G>A (p.Asp90Asn)

Gene:

KMT5B:lysine methyltransferase 5B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.2

Genomic location:

Preferred name:

NM_017635.5(KMT5B):c.268G>A (p.Asp90Asn)

HGVS:

NC_000011.10:g.68185821C>T
NG_052873.1:g.32952G>A
NM_001300907.1:c.-317G>A
NM_001300908.2:c.-400G>A
NM_001300909.2:c.268G>A
NM_001363566.2:c.268G>A
NM_001369424.1:c.-396G>A
NM_001369425.1:c.55G>A
NM_001369426.1:c.268G>A
NM_001369427.1:c.268G>A
NM_001369428.1:c.-610G>A
NM_001369429.1:c.-209+4096G>A
NM_001369430.1:c.-327G>A
NM_001369431.1:c.-396G>A
NM_001369432.1:c.-396G>A
NM_001369433.1:c.-911G>A
NM_016028.4:c.268G>A
NM_017635.5:c.268G>AMANE SELECT
NP_001287838.1:p.Asp90Asn
NP_001350495.1:p.Asp90Asn
NP_001356354.1:p.Asp19Asn
NP_001356355.1:p.Asp90Asn
NP_001356356.1:p.Asp90Asn
NP_057112.3:p.Asp90Asn
NP_060105.3:p.Asp90Asn
NC_000011.9:g.67953288C>T
NR_161378.1:n.516G>A
NR_161379.1:n.516G>A
NR_161380.1:n.516G>A

Protein change:

D19N

Links:

dbSNP: rs2153068007

NCBI 1000 Genomes Browser:

rs2153068007

Molecular consequence:

NM_001300907.1:c.-317G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001300908.2:c.-400G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369424.1:c.-396G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369428.1:c.-610G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369430.1:c.-327G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369431.1:c.-396G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369432.1:c.-396G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369433.1:c.-911G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001369429.1:c.-209+4096G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001300909.2:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363566.2:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369425.1:c.55G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369426.1:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369427.1:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_016028.4:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_017635.5:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_161378.1:n.516G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_161379.1:n.516G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_161380.1:n.516G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Intellectual disability, autosomal dominant 51
Synonyms:: MENTAL RETARDATION, AUTOSOMAL DOMINANT 51; INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 51
Identifiers:: MONDO: MONDO:0030917; MedGen: C4540474; OMIM: 617788

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002098002	New York Genome Center - CSER-NYCKidSeq	criteria provided, single submitter (NYGC Assertion Criteria 2020)	Uncertain significance (Jun 18, 2020)	inherited	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002098002

New York Genome Center - CSER-NYCKidSeq

criteria provided, single submitter

(NYGC Assertion Criteria 2020)

Uncertain significance
(Jun 18, 2020)

inherited

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002098002.1

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

Description

The inherited heterozygous p.Asp90Asn variant identified in KMT5B has not been reported in affected individuals in the literature. The variant is absent from the gnomAD(v3) database indicating it is an extremely rare allele in the general population represented in the database. In silico tools provide conflicting interpretations about potential pathogenicity of this variant. Based on the available evidence, the inherited heterozygous p.Asp90Asn variant in the KMT5B gene is assessed as a variant of uncertain significance.

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

Last Updated: Dec 24, 2023

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