NM_000969.5(RPL5):c.169_172del (p.Asn57fs) AND Diamond-Blackfan anemia 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 13, 2019
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:: RCV000761557.10

Allele description [Variation Report for NM_000969.5(RPL5):c.169_172del (p.Asn57fs)]

NM_000969.5(RPL5):c.169_172del (p.Asn57fs)

Genes:

DIPK1A:divergent protein kinase domain 1A [Gene - OMIM - HGNC]
RPL5:ribosomal protein L5 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1p22.1

Genomic location:

Preferred name:

NM_000969.5(RPL5):c.169_172del (p.Asn57fs)

HGVS:

NC_000001.11:g.92833640_92833643del
NG_011779.2:g.6655_6658del
NG_033051.1:g.132883_132886del
NM_000969.5:c.169_172delMANE SELECT
NM_001252273.2:c.475-606_475-603del
NP_000960.2:p.Asn57fs
LRG_1155t1:c.169_172del
LRG_1155:g.6655_6658del
LRG_1155p1:p.Asn57fs
NC_000001.10:g.93299194_93299197del
NC_000001.10:g.93299197_93299200del
NC_000001.11:g.92833637_92833640delACAA
NM_000969.3:c.169_172del
NM_000969.3:c.169_172delAACA
NM_000969.5:c.169_172delAACAMANE SELECT
NR_146333.1:n.298_301del
p.N57Qfs*12

Protein change:

N57fs

Links:

dbSNP: rs1558284033

NCBI 1000 Genomes Browser:

rs1558284033

Molecular consequence:

NM_000969.5:c.169_172del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001252273.2:c.475-606_475-603del - intron variant - [Sequence Ontology: SO:0001627]
NR_146333.1:n.298_301del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Functional consequence:

Unknown function

Observations:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000889935	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 13, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000889935

Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 13, 2019)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
Indian	germline	yes	1	not provided	not provided	not provided	not provided	clinical 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 Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV000889935.1

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

Description

The p.N57Qfs*12 variant in the RPL5 gene is a de novo frameshift variant, which is absent in the gnomAD database and has previously been reported as a pathogenic variant in the ClinVar database (Accession: RCV000702906.1). In summary, the p.N57Qfs*12 variant meets the ACMG criteria to be classified as pathogenic based upon inheritance model, absence from controls and previous ClinVar submission.

#	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		1	not provided	not provided	not provided

Last Updated: May 7, 2024

ClinVar

Relating variation to medicine