NM_000969.5(RPL5):c.169_172del (p.Asn57fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Feb 4, 2019
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:: RCV001008074.23

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001167812	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Feb 4, 2019)	germline	clinical testing	Citation Link,
SCV001245631	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jun 1, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001167812

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Feb 4, 2019)

germline

clinical testing

Citation Link,

SCV001245631

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Pathogenic
(Jun 1, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001167812.1

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

Description

The c.169_172delAACA variant has been reported previously in association with Diamond-Blackfan anemia, including an apparently de novo occurrence (Cmejla et al., 2009; Quarello et al., 2010; Gerrard et al., 2013). The deletion causes a frameshift starting with codon Asparagine 57, changes this amino acid to a Glutamic acid residue and creates a premature Stop codon at position 12 of the new reading frame, denoted p.Asn57GlufsX12. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The variant is not observed in large population cohorts (Lek et al., 2016). In summary, we consider the variant to be pathogenic.

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001245631.20

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

#	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

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