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NM_016038.4(SBDS):c.258+2T>C AND Aplastic anemia, susceptibility to

Germline classification:
risk factor (1 submission)
Last evaluated:
Aug 15, 2007
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000003348.9

Allele description [Variation Report for NM_016038.4(SBDS):c.258+2T>C]

NM_016038.4(SBDS):c.258+2T>C

Gene:
SBDS:SBDS ribosome maturation factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q11.21
Genomic location:
Preferred name:
NM_016038.4(SBDS):c.258+2T>C
Other names:
c.258+2T>C
HGVS:
  • NC_000007.14:g.66994210A>G
  • NG_007277.1:g.6392T>C
  • NG_033069.1:g.2406A>G
  • NM_016038.4:c.258+2T>CMANE SELECT
  • LRG_104t1:c.258+2T>C
  • LRG_104:g.6392T>C
  • NC_000007.13:g.66459197A>G
  • NM_016038.2:c.258+2T>C
  • NM_016038.2:c.[258+2T>C]
  • NM_016038.3:c.258+2T>C
Nucleotide change:
IVS2DS, T-C, +2
Links:
OMIM: 607444.0002; dbSNP: rs113993993
NCBI 1000 Genomes Browser:
rs113993993
Molecular consequence:
  • NM_016038.4:c.258+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
Functional consequence:
effect on RNA splicing [Variation Ontology: 0362]

Condition(s)

Name:
Aplastic anemia, susceptibility to
Identifiers:
MONDO: MONDO:0800414; MedGen: C2684859

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000023506OMIM
no assertion criteria provided
risk factor
(Aug 15, 2007)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutations in SBDS are associated with Shwachman-Diamond syndrome.

Boocock GR, Morrison JA, Popovic M, Richards N, Ellis L, Durie PR, Rommens JM.

Nat Genet. 2003 Jan;33(1):97-101. Epub 2002 Dec 23.

PubMed [citation]
PMID:
12496757

Hematologic abnormalities in Shwachman Diamond syndrome: lack of genotype-phenotype relationship.

Kuijpers TW, Alders M, Tool AT, Mellink C, Roos D, Hennekam RC.

Blood. 2005 Jul 1;106(1):356-61. Epub 2005 Mar 15.

PubMed [citation]
PMID:
15769891
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000023506.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

Shwachman-Diamond Syndrome 1

For discussion of the splice site mutation in the SBDS gene (IVS2DS+2T-C) that was found in compound heterozygous state in patients with Shwachman-Diamond syndrome (SDS1; 260400) by Boocock et al. (2003) and Kuijpers et al. (2005), see 607444.0001. Boocock et al. (2003) referred to this mutation as 258+2T-C.

Nakashima et al. (2004) identified this mutation in affected members of 4 Japanese families with SDS, making it the most prevalent mutation. Recurrent gene conversion was considered the most likely explanation for the recurrence, rather than founder effect.

Aplastic Anemia, Susceptibility to

Calado et al. (2007) identified heterozygosity for the IVS2DS+2T-C mutation in 4 of 91 unrelated patients with aplastic anemia (609135). These patients were younger on average (5 to 19 years) compared to other patients with aplastic anemia. Two mothers tested were carriers of the mutation; these 2 and another mother who was not tested had histories of subclinical mild anemia. Heterozygous mutation carriers had partial loss of SBDS protein expression, indicating haploinsufficiency. Although telomere shortening was observed in patients' granulocytes, lymphocytes had normal telomere length. None of the patients with aplastic anemia had pancreatic exocrine failure or skeletal anomalies as seen in SDS. One of the 4 probands was also heterozygous for a presumed pathogenic variant in the TERT gene (187270).

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

Last Updated: May 12, 2024