NM_001014.5(RPS10):c.71A>G (p.Lys24Arg) AND Diamond-Blackfan anemia 9

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 20, 2019
Review status:: criteria provided, conflicting classifications

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:: RCV000309035.9

Allele description [Variation Report for NM_001014.5(RPS10):c.71A>G (p.Lys24Arg)]

NM_001014.5(RPS10):c.71A>G (p.Lys24Arg)

Genes:

RPS10-NUDT3:RPS10-NUDT3 readthrough [Gene - HGNC]
RPS10:ribosomal protein S10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.31

Genomic location:

Preferred name:

NM_001014.5(RPS10):c.71A>G (p.Lys24Arg)

HGVS:

NC_000006.12:g.34425151T>C
NG_023200.1:g.5949A>G
NM_001014.5:c.71A>GMANE SELECT
NM_001202470.3:c.71A>G
NM_001203245.3:c.71A>G
NM_001204091.2:c.71A>G
NP_001005.1:p.Lys24Arg
NP_001189399.1:p.Lys24Arg
NP_001190174.1:p.Lys24Arg
NP_001191020.1:p.Lys24Arg
LRG_1138t1:c.71A>G
LRG_1138:g.5949A>G
LRG_1138p1:p.Lys24Arg
NC_000006.11:g.34392928T>C
NM_001014.4:c.71A>G
NM_001202470.2:c.71A>G

Protein change:

K24R

Links:

dbSNP: rs201147592

NCBI 1000 Genomes Browser:

rs201147592

Molecular consequence:

NM_001014.5:c.71A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001202470.3:c.71A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001203245.3:c.71A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001204091.2:c.71A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Diamond-Blackfan anemia 9 (DBA9)
Identifiers:: MONDO: MONDO:0013216; MedGen: C2750081; Orphanet: 124; OMIM: 613308

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000462637	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV001481486	Baylor Genetics - CSER-TexasKidsCanSeq	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 20, 2019)	maternal	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

SCV000462637

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

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

Citation Link,

SCV001481486

Baylor Genetics - CSER-TexasKidsCanSeq

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 20, 2019)

maternal

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Ribosomal protein genes RPS10 and RPS26 are commonly mutated in Diamond-Blackfan anemia.

Doherty L, Sheen MR, Vlachos A, Choesmel V, O'Donohue MF, Clinton C, Schneider HE, Sieff CA, Newburger PE, Ball SE, Niewiadomska E, Matysiak M, Glader B, Arceci RJ, Farrar JE, Atsidaftos E, Lipton JM, Gleizes PE, Gazda HT.

Am J Hum Genet. 2010 Feb 12;86(2):222-8. doi: 10.1016/j.ajhg.2009.12.015. Epub 2010 Jan 28. Erratum in: Am J Hum Genet. 2010 Apr 9;86(4):655.

PubMed [citation]

PMID:: 20116044
PMCID:: PMC2820177

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 Illumina Laboratory Services, Illumina, SCV000462637.3

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics - CSER-TexasKidsCanSeq, SCV001481486.2

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

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 1, 2024

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