NM_014140.4(SMARCAL1):c.1503del (p.Pro502fs) AND Schimke immuno-osseous dysplasia

Clinical significance:Pathogenic (Last evaluated: Oct 11, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001205978.2

Allele description [Variation Report for NM_014140.4(SMARCAL1):c.1503del (p.Pro502fs)]

NM_014140.4(SMARCAL1):c.1503del (p.Pro502fs)

Gene:
SMARCAL1:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2q35
Genomic location:
Preferred name:
NM_014140.4(SMARCAL1):c.1503del (p.Pro502fs)
HGVS:
  • NC_000002.12:g.216435355del
  • NG_009771.1:g.27942del
  • NM_001127207.2:c.1503del
  • NM_014140.4:c.1503delMANE SELECT
  • NP_001120679.1:p.Pro502fs
  • NP_054859.2:p.Pro502fs
  • LRG_108t1:c.1503del
  • LRG_108:g.27942del
  • NC_000002.11:g.217300078del
  • NM_014140.3:c.1503del
Protein change:
P502fs
Molecular consequence:
  • NM_001127207.2:c.1503del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_014140.4:c.1503del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Schimke immuno-osseous dysplasia (SIOD)
Synonyms:
Spondyloepiphyseal dysplasia nephrotic syndrome; Schimke syndrome; Schimke immunoosseous dysplasia
Identifiers:
MONDO: MONDO:0009458; MedGen: C0877024; Orphanet: 1830; OMIM: 242900

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001377262Invitaecriteria provided, single submitter
Pathogenic
(Oct 11, 2019)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutant chromatin remodeling protein SMARCAL1 causes Schimke immuno-osseous dysplasia.

Boerkoel CF, Takashima H, John J, Yan J, Stankiewicz P, Rosenbarker L, André JL, Bogdanovic R, Burguet A, Cockfield S, Cordeiro I, Fründ S, Illies F, Joseph M, Kaitila I, Lama G, Loirat C, McLeod DR, Milford DV, Petty EM, Rodrigo F, Saraiva JM, et al.

Nat Genet. 2002 Feb;30(2):215-20. Epub 2002 Jan 22.

PubMed [citation]
PMID:
11799392

Schimke Immunoosseous Dysplasia.

Morimoto M, Lewis DB, Lücke T, Boerkoel CF.

2002 Oct 1 [updated 2016 Feb 11]. In: Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Mirzaa G, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2021.

PubMed [citation]
PMID:
20301550
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001377262.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Pro502Hisfs*3) in the SMARCAL1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SMARCAL1-related conditions. Loss-of-function variants in SMARCAL1 are known to be pathogenic (PMID: 11799392, 20301550). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 7, 2021

Support Center