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NM_001098426.2(SMARCD2):c.401+2T>C AND Specific granule deficiency 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 25, 2017
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:
RCV000490561.1

Allele description [Variation Report for NM_001098426.2(SMARCD2):c.401+2T>C]

NM_001098426.2(SMARCD2):c.401+2T>C

Gene:
SMARCD2:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q23.3
Genomic location:
Preferred name:
NM_001098426.2(SMARCD2):c.401+2T>C
Other names:
IVS2+2_T>C
HGVS:
  • NC_000017.11:g.63837439A>G
  • NG_053004.1:g.10553T>C
  • NM_001098426.2:c.401+2T>CMANE SELECT
  • NM_001330439.1:c.176+2T>C
  • NM_001330440.2:c.257+2T>C
  • NC_000017.10:g.61914799A>G
  • NM_001098426.1:c.401+2T>C
Nucleotide change:
IVS2DS, T-C, +2
Links:
OMIM: 601736.0003; dbSNP: rs1057518733
NCBI 1000 Genomes Browser:
rs1057518733
Molecular consequence:
  • NM_001098426.2:c.401+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001330439.1:c.176+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001330440.2:c.257+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Specific granule deficiency 2 (SGD2)
Identifiers:
MONDO: MONDO:0044208; MedGen: C4479548; OMIM: 617475

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000579215OMIM
no assertion criteria provided
Pathogenic
(May 25, 2017) 		germlineliterature only

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

Help

Summary from all submissions

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

Citations

PubMed

Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes.

Witzel M, Petersheim D, Fan Y, Bahrami E, Racek T, Rohlfs M, Puchałka J, Mertes C, Gagneur J, Ziegenhain C, Enard W, Stray-Pedersen A, Arkwright PD, Abboud MR, Pazhakh V, Lieschke GJ, Krawitz PM, Dahlhoff M, Schneider MR, Wolf E, Horny HP, Schmidt H, et al.

Nat Genet. 2017 May;49(5):742-752. doi: 10.1038/ng.3833. Epub 2017 Apr 3.

PubMed [citation]
PMID:
28369036
PMCID:
PMC5885283

Details of each submission

From OMIM, SCV000579215.1

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

Description

In a boy, born of consanguineous Lebanese parents, with specific granule deficiency-2 (SGD2; 617475), Witzel et al. (2017) identified a homozygous T-to-C transition (c.401+2T-C, NM_001098426.1), in intron 2 of the SMARCD2 gene, resulting in a splice site alteration, a frameshift, and premature termination (Arg73ValfsTer8). The mutation segregated with the disorder in the family. Immunoblot analysis showed absence of the SMARCD2 protein in patient-derived cells. Expression of the truncated isoform in 293T cells showed that it was unable to coprecipitate with other SMARCD proteins, indicating a loss of function.

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

Last Updated: Aug 5, 2023