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NM_001003694.2(BRPF1):c.898G>A (p.Val300Met) AND Intellectual developmental disorder with dysmorphic facies and ptosis

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 18, 2022
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:
RCV002272688.2

Allele description [Variation Report for NM_001003694.2(BRPF1):c.898G>A (p.Val300Met)]

NM_001003694.2(BRPF1):c.898G>A (p.Val300Met)

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.898G>A (p.Val300Met)
HGVS:
  • NC_000003.12:g.9739297G>A
  • NG_052955.1:g.12569G>A
  • NM_001003694.2:c.898G>AMANE SELECT
  • NM_001319049.2:c.898G>A
  • NM_001319050.2:c.898G>A
  • NM_004634.3:c.898G>A
  • NP_001003694.1:p.Val300Met
  • NP_001305978.1:p.Val300Met
  • NP_001305979.1:p.Val300Met
  • NP_004625.2:p.Val300Met
  • NC_000003.11:g.9780981G>A
  • NR_160918.1:n.1312G>A
Protein change:
V300M
Links:
dbSNP: rs2125500407
NCBI 1000 Genomes Browser:
rs2125500407
Molecular consequence:
  • NM_001003694.2:c.898G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001319049.2:c.898G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001319050.2:c.898G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004634.3:c.898G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_160918.1:n.1312G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Intellectual developmental disorder with dysmorphic facies and ptosis (IDDDFP)
Identifiers:
MONDO: MONDO:0015022; MedGen: C4310617; OMIM: 617333

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002556708Genetics and Molecular Pathology, SA Pathology

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jan 18, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 Genetics and Molecular Pathology, SA Pathology, SCV002556708.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The BRPF1 c.898G>A variant is classified as LIKELY PATHOGENIC (PP3, PM2, PS2) The BRPF1 c.898G>A variant is a single nucleotide change in exon 3/14 of the BRPF1 gene, which is predicted to change the amino acid valine at position 300 in the protein to methionine. This variant is de novo in this patient (PS2). This variant has not been reported in dbSNP and is absent from population databases (PM2). This variant has not been reported in the ClinVar or HGMD disease databases. Computational predictions support a deleterious effect on the gene or gene product (PP3).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 24, 2023