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NM_001022.4(RPS19):c.316del (p.Ala106fs) AND Diamond-Blackfan anemia 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 25, 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:
RCV002790030.3

Allele description [Variation Report for NM_001022.4(RPS19):c.316del (p.Ala106fs)]

NM_001022.4(RPS19):c.316del (p.Ala106fs)

Gene:
RPS19:ribosomal protein S19 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19q13.2
Genomic location:
Preferred name:
NM_001022.4(RPS19):c.316del (p.Ala106fs)
Other names:
NM_001321485.2:c.329del
HGVS:
  • NC_000019.10:g.41869174del
  • NG_007080.3:g.14257del
  • NM_001022.4:c.316delMANE SELECT
  • NM_001321483.2:c.316del
  • NM_001321484.2:c.316del
  • NM_001321485.2:c.329del
  • NP_001013.1:p.Ala106fs
  • NP_001308412.1:p.Ala106fs
  • NP_001308413.1:p.Ala106fs
  • NP_001308414.1:p.Ser110fs
  • LRG_1144t1:c.316del
  • LRG_1144:g.14257del
  • LRG_1144p1:p.Ala106fs
  • NC_000019.9:g.42373244del
Protein change:
A106fs
Molecular consequence:
  • NM_001022.4:c.316del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001321483.2:c.316del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001321484.2:c.316del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001321485.2:c.329del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Diamond-Blackfan anemia 1 (DBA1)
Identifiers:
MONDO: MONDO:0007110; MedGen: C2676137; Orphanet: 124; OMIM: 105650

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003761399Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jan 25, 2023) 		germlinecuration

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

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 Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV003761399.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

The heterozygous p.Ala106ProfsTer5 variant in RPS19 was identified by our study in one individual with Diamond-Blackfan anemia. Trio exome analysis showed this variant to be de novo. The p.Ala106ProfsTer5 variant in RPS19 has not been previously reported in individuals with Diamond-Blackfan anemia 1. This variant was absent from large population studies. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 106 and leads to a premature termination codon 5 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Heterozygous loss of function of the RPS19 gene is an established disease mechanism in autosomal dominant Diamond-Blackfan anemia 1. In summary, this variant meets criteria to be classified as pathogenic for Diamond-Blackfan anemia 1. ACMG/AMP Criteria applied: PVS1, PS2_Supporting, PM2_Supporting (Richards 2015).

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

Last Updated: Jun 23, 2024