NM_014140.4(SMARCAL1):c.429_430insTGATTTA (p.Gly144Ter) AND Schimke immuno-osseous dysplasia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 10, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003057113.3

Allele description [Variation Report for NM_014140.4(SMARCAL1):c.429_430insTGATTTA (p.Gly144Ter)]

NM_014140.4(SMARCAL1):c.429_430insTGATTTA (p.Gly144Ter)

Gene:

SMARCAL1:SNF2 related chromatin remodeling annealing helicase 1 [Gene - OMIM - HGNC]

Variant type:

Insertion

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_014140.4(SMARCAL1):c.429_430insTGATTTA (p.Gly144Ter)

HGVS:

NC_000002.12:g.216415133_216415134insTGATTTA
NG_009771.1:g.7720_7721insTGATTTA
NM_001127207.2:c.429_430insTGATTTA
NM_014140.4:c.429_430insTGATTTAMANE SELECT
NP_001120679.1:p.Gly144Ter
NP_054859.2:p.Gly144Ter
NP_054859.2:p.Gly144Terfs
LRG_108t1:c.429_430insTGATTTA
LRG_108:g.7720_7721insTGATTTA
LRG_108p1:p.Gly144Terfs
NC_000002.11:g.217279853_217279854insTTATGAT
NC_000002.11:g.217279856_217279857insTGATTTA
NM_014140.3:c.429_430insTGATTTA

Protein change:

G144*

Molecular consequence:

NM_001127207.2:c.429_430insTGATTTA - nonsense - [Sequence Ontology: SO:0001587]
NM_014140.4:c.429_430insTGATTTA - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003343719	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 10, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11799392, 20301550, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003343719

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 10, 2022)

germline

clinical testing

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

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

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.

Lippner E, Lücke T, Salgado C, Boerkoel C, Lewis DB.

2002 Oct 1 [updated 2023 Mar 30]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 20301550

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003343719.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly144*) in the SMARCAL1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SMARCAL1 are known to be pathogenic (PMID: 11799392, 20301550). This variant has not been reported in the literature in individuals affected with SMARCAL1-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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 29, 2024

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