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

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 28, 2024
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:: RCV001493828.9

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
Synonyms:: Blackfan Diamond syndrome; Anemia congenital erythroid hypoplastic; Aregenerative anemia chronic congenital; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015253; MeSH: D029503; MedGen: C1260899; Orphanet: 124; OMIM: PS105650; Human Phenotype Ontology: HP:0004810

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001698468	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 28, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002668557	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jul 6, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001698468

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 28, 2024)

germline

clinical testing

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

SCV002668557

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jul 6, 2017)

germline

clinical testing

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

Citation Link

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

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

Details of each submission

From Invitae, SCV001698468.4

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

#	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 Ambry Genetics, SCV002668557.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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

Last Updated: Sep 1, 2024

ClinVar

Relating variation to medicine