NM_001003694.2(BRPF1):c.1182_1183del (p.Ala396fs) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Aug 21, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002068746.19

Allele description [Variation Report for NM_001003694.2(BRPF1):c.1182_1183del (p.Ala396fs)]

NM_001003694.2(BRPF1):c.1182_1183del (p.Ala396fs)

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.1182_1183del (p.Ala396fs)

HGVS:

NC_000003.12:g.9739581_9739582del
NG_052955.1:g.12853_12854del
NM_001003694.2:c.1182_1183delMANE SELECT
NM_001319049.2:c.1182_1183del
NM_001319050.2:c.1182_1183del
NM_004634.3:c.1182_1183del
NP_001003694.1:p.Ala396fs
NP_001305978.1:p.Ala396fs
NP_001305979.1:p.Ala396fs
NP_004625.2:p.Ala396fs
NC_000003.11:g.9781265_9781266del
NM_001003694.1:c.1182_1183del
NM_001003694.1:c.1182_1183delAG
NM_001003694.2:c.1182_1183delAGMANE SELECT
NR_160918.1:n.1596_1597del

Protein change:

A396fs

Links:

dbSNP: rs1575155995

NCBI 1000 Genomes Browser:

rs1575155995

Molecular consequence:

NM_001003694.2:c.1182_1183del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001319049.2:c.1182_1183del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001319050.2:c.1182_1183del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004634.3:c.1182_1183del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_160918.1:n.1596_1597del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Functional consequence:

loss_of_function_variant [Sequence Ontology: SO:0002054]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

hypothetical protein CRG98_040530 [Punica granatum]
hypothetical protein CRG98_040530 [Punica granatum]
gi|1305222909|gb|PKI39106.1||gnl|WG L|PGP040530

Protein
Abutilon arboreum (0)
Nucleotide
Acacia suaveolens AND 1[s_discriminator] (0)
dbGaP
Acacia suaveolens (7)
Identical Protein Groups
Uncultured Glomeromycota clone K93_4 18S ribosomal RNA gene, partial sequence
Uncultured Glomeromycota clone K93_4 18S ribosomal RNA gene, partial sequence
gi|479015729|gb|JX297000.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002496775	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Aug 1, 2023)	germline	clinical testing	Citation Link,
SCV002502894	AiLife Diagnostics, AiLife Diagnostics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 3, 2021)	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 32652122, 25741868
SCV004028156	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Aug 21, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002496775

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Aug 1, 2023)

germline

clinical testing

Citation Link,

SCV002502894

AiLife Diagnostics, AiLife Diagnostics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 3, 2021)

de novo

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV004028156

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Aug 21, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A de novo BRPF1 variant in a case of Sudden Unexplained Death in Childhood.

Keywan C, Holm IA, Poduri A, Brownstein CA, Alexandrescu S, Chen J, Geffre C, Goldstein RD.

Eur J Med Genet. 2020 Sep;63(9):104002. doi: 10.1016/j.ejmg.2020.104002. Epub 2020 Jul 8.

PubMed [citation]

PMID:: 32652122
PMCID:: PMC7469702

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

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV002496775.17

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

Description

BRPF1: PVS1, PS2, PM2, PS4:Moderate

#	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		2	not provided	not provided	not provided

From AiLife Diagnostics, AiLife Diagnostics, SCV002502894.1

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

#	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		1	not provided	not provided	not provided

From GeneDx, SCV004028156.1

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 32652122, 35027292, 33004838)

#	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: Oct 8, 2024

ClinVar

Relating variation to medicine