NM_014140.4(SMARCAL1):c.313C>T (p.Pro105Ser) AND Schimke immuno-osseous dysplasia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 4, 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:: RCV002761689.3

Allele description [Variation Report for NM_014140.4(SMARCAL1):c.313C>T (p.Pro105Ser)]

NM_014140.4(SMARCAL1):c.313C>T (p.Pro105Ser)

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.313C>T (p.Pro105Ser)

HGVS:

NC_000002.12:g.216415017C>T
NG_009771.1:g.7604C>T
NM_001127207.2:c.313C>T
NM_014140.4:c.313C>TMANE SELECT
NP_001120679.1:p.Pro105Ser
NP_054859.2:p.Pro105Ser
NP_054859.2:p.Pro105Ser
LRG_108t1:c.313C>T
LRG_108:g.7604C>T
LRG_108p1:p.Pro105Ser
NC_000002.11:g.217279740C>T
NM_014140.3:c.313C>T

Protein change:

P105S

Molecular consequence:

NM_001127207.2:c.313C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_014140.4:c.313C>T - missense variant - [Sequence Ontology: SO:0001583]

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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rplR [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
rplR [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
Gene ID:1254947

Gene
Nothofagus pumilio (1)
Taxonomy
nssv2940733 (2)
dbVar

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003027400	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 4, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003027400

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 4, 2022)

germline

clinical testing

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

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, SCV003027400.2

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

Description

This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 105 of the SMARCAL1 protein (p.Pro105Ser). This variant is present in population databases (rs372708949, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with SMARCAL1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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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