NM_001003694.2(BRPF1):c.28_29del (p.Phe10fs) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 2, 2023
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:: RCV000624851.4

Allele description [Variation Report for NM_001003694.2(BRPF1):c.28_29del (p.Phe10fs)]

NM_001003694.2(BRPF1):c.28_29del (p.Phe10fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3p25.3

Genomic location:

Preferred name:

NM_001003694.2(BRPF1):c.28_29del (p.Phe10fs)

HGVS:

NC_000003.12:g.9734168_9734169del
NG_052955.1:g.7440_7441del
NM_001003694.2:c.28_29delMANE SELECT
NM_001319049.2:c.28_29del
NM_001319050.2:c.28_29del
NM_004634.3:c.28_29del
NP_001003694.1:p.Phe10fs
NP_001305978.1:p.Phe10fs
NP_001305979.1:p.Phe10fs
NP_004625.2:p.Phe10fs
NC_000003.11:g.9775852_9775853del
NM_001003694.1:c.28_29delTT
NR_160918.1:n.442_443del

Protein change:

F10fs

Links:

dbSNP: rs1553693712

NCBI 1000 Genomes Browser:

rs1553693712

Molecular consequence:

NM_001003694.2:c.28_29del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001319049.2:c.28_29del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001319050.2:c.28_29del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004634.3:c.28_29del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_160918.1:n.442_443del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000743078	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Mar 2, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25954003, 27618451, 28490743 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000743078

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Mar 2, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, et al.

Science. 2015 May 8;348(6235):666-9. doi: 10.1126/science.1261877.

PubMed [citation]

PMID:: 25954003
PMCID:: PMC4537935

The rules and impact of nonsense-mediated mRNA decay in human cancers.

Lindeboom RG, Supek F, Lehner B.

Nat Genet. 2016 Oct;48(10):1112-8. doi: 10.1038/ng.3664. Epub 2016 Sep 12.

PubMed [citation]

PMID:: 27618451
PMCID:: PMC5045715

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV000743078.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The c.28_29delTT (p.F10Lfs*8) alteration, located in exon 2 (coding exon 1) of the BRPF1 gene, consists of a deletion of 2 nucleotides from position 28 to 29, causing a translational frameshift with a predicted alternate stop codon after 8 amino acids. The predicted stop codon occurs in the 5' end of the BRPF1 gene. Premature termination codons in the 5’ end of a gene have been reported to escape nonsense-mediated mRNA decay and/or lead to re-initiation (Rivas, 2015; Lindeboom, 2016; Rhee, 2017). Direct evidence for this alteration is unavailable; however, premature termination codons are typically deleterious in nature. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the available evidence, this alteration is classified as pathogenic.

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

Last Updated: May 1, 2024

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