NM_014140.4(SMARCAL1):c.2556T>C (p.Val852=) AND Schimke immuno-osseous dysplasia

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Mar 10, 2023
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:: RCV001414494.16

Allele description [Variation Report for NM_014140.4(SMARCAL1):c.2556T>C (p.Val852=)]

NM_014140.4(SMARCAL1):c.2556T>C (p.Val852=)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_014140.4(SMARCAL1):c.2556T>C (p.Val852=)

HGVS:

NC_000002.12:g.216478230T>C
NG_009771.1:g.70817T>C
NM_001127207.2:c.2556T>C
NM_014140.4:c.2556T>CMANE SELECT
NP_001120679.1:p.Val852=
NP_054859.2:p.Val852=
LRG_108t1:c.2556T>C
LRG_108:g.70817T>C
NC_000002.11:g.217342953T>C
NM_014140.3:c.2556T>C

Links:

dbSNP: rs1574485907

NCBI 1000 Genomes Browser:

rs1574485907

Molecular consequence:

NM_001127207.2:c.2556T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_014140.4:c.2556T>C - synonymous variant - [Sequence Ontology: SO:0001819]

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

Recent activity

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G patch domain-containing protein 2 isoform X6 [Homo sapiens]
G patch domain-containing protein 2 isoform X6 [Homo sapiens]
gi|2217268618|ref|XP_047279757.1|

Protein
Probable galacturonosyltransferase 4 isoform 1 [Zea mays]
Probable galacturonosyltransferase 4 isoform 1 [Zea mays]
gi|2305409556|ref|NP_001148932.2|

Protein
uronyl 2-sulfotransferase a isoform X1 [Hippoglossus stenolepis]
uronyl 2-sulfotransferase a isoform X1 [Hippoglossus stenolepis]
gi|1863369138|ref|XP_034999989.1|

Protein
Tssr128526 AND (alive[prop]) (0)
Gene
CASP8 and FADD-like apoptosis regulator isoform X1 [Mus musculus]
CASP8 and FADD-like apoptosis regulator isoform X1 [Mus musculus]
gi|568905660|ref|XP_006495698.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001616633	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Mar 10, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002076335	Natera, Inc.	no assertion criteria provided	Likely benign (Mar 16, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001616633

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Mar 10, 2023)

germline

clinical testing

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

SCV002076335

Natera, Inc.

no assertion criteria provided

Likely benign
(Mar 16, 2021)

germline

clinical testing

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001616633.4

#	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 Natera, Inc., SCV002076335.1

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

#	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: Nov 10, 2024

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