NM_001003694.2(BRPF1):c.1218C>G (p.Tyr406Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 26, 2018
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:: RCV000579243.1

Allele description [Variation Report for NM_001003694.2(BRPF1):c.1218C>G (p.Tyr406Ter)]

NM_001003694.2(BRPF1):c.1218C>G (p.Tyr406Ter)

Gene:

BRPF1:bromodomain and PHD finger containing 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.3

Genomic location:

Preferred name:

NM_001003694.2(BRPF1):c.1218C>G (p.Tyr406Ter)

HGVS:

NC_000003.12:g.9739617C>G
NG_052955.1:g.12889C>G
NM_001003694.2:c.1218C>GMANE SELECT
NM_001319049.2:c.1218C>G
NM_001319050.2:c.1218C>G
NM_004634.3:c.1218C>G
NP_001003694.1:p.Tyr406Ter
NP_001305978.1:p.Tyr406Ter
NP_001305979.1:p.Tyr406Ter
NP_004625.2:p.Tyr406Ter
NC_000003.11:g.9781301C>G
NM_001003694.1:c.1218C>G
NR_160918.1:n.1632C>G

Protein change:

Y406*

Links:

dbSNP: rs1553695222

NCBI 1000 Genomes Browser:

rs1553695222

Molecular consequence:

NR_160918.1:n.1632C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001003694.2:c.1218C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001319049.2:c.1218C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001319050.2:c.1218C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_004634.3:c.1218C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000681382	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jan 26, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000681382

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jan 26, 2018)

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, SCV000681382.2

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

Description

The Y406X variant in the BRPF1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The Y406X variant is not observed in large population cohorts (Lek et al., 2016). We interpret Y406X as a pathogenic variant.

#	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: Apr 23, 2022

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