NM_017635.5(KMT5B):c.2434C>T (p.Arg812Ter) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 4, 2019
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:: RCV000760963.1

Allele description [Variation Report for NM_017635.5(KMT5B):c.2434C>T (p.Arg812Ter)]

NM_017635.5(KMT5B):c.2434C>T (p.Arg812Ter)

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.2434C>T (p.Arg812Ter)

HGVS:

NC_000011.10:g.68157912G>A
NG_052873.1:g.60861C>T
NM_001300907.1:c.1918C>T
NM_001300908.2:c.1714C>T
NM_001369426.1:c.2434C>T
NM_001369428.1:c.1918C>T
NM_001369429.1:c.1918C>T
NM_001369430.1:c.1918C>T
NM_001369431.1:c.1918C>T
NM_001369432.1:c.1918C>T
NM_001369433.1:c.1918C>T
NM_017635.5:c.2434C>TMANE SELECT
NP_001287836.1:p.Arg640Ter
NP_001287837.1:p.Arg572Ter
NP_001356355.1:p.Arg812Ter
NP_001356357.1:p.Arg640Ter
NP_001356358.1:p.Arg640Ter
NP_001356359.1:p.Arg640Ter
NP_001356360.1:p.Arg640Ter
NP_001356361.1:p.Arg640Ter
NP_001356362.1:p.Arg640Ter
NP_060105.3:p.Arg812Ter
NC_000011.9:g.67925379G>A
NM_017635.3:c.2434C>T

Protein change:

R572*

Links:

dbSNP: rs1565212298

NCBI 1000 Genomes Browser:

rs1565212298

Molecular consequence:

NM_001300907.1:c.1918C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001300908.2:c.1714C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001369426.1:c.2434C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001369428.1:c.1918C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001369429.1:c.1918C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001369430.1:c.1918C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001369431.1:c.1918C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001369432.1:c.1918C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001369433.1:c.1918C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_017635.5:c.2434C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Perca fluviatilis voucher Pf_M1, whole genome shotgun sequencing project
Perca fluviatilis voucher Pf_M1, whole genome shotgun sequencing project
gi|1802907429|gb|VHII00000000.1|VHI 0000

Nucleotide
NADH dehydrogenase subunit 4L (mitochondrion) [Perca fluviatilis]
NADH dehydrogenase subunit 4L (mitochondrion) [Perca fluviatilis]
gi|1802882662|gb|KAF1371393.1||gnl| HII|PFLUV_P0027900

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000890860	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Feb 4, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000890860

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Feb 4, 2019)

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, SCV000890860.1

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

Description

A variant that is likely pathogenic has been identified in the KMT5B gene. The R812X variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R812X variant is not observed in large population cohorts (Lek et al., 2016). The R812X nonsense variant is predicted to cause loss of normal protein function through protein truncation, as the last 74 amino acids are lost. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

#	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: May 7, 2024

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