NM_003070.5(SMARCA2):c.3485G>A (p.Arg1162His) AND Nicolaides-Baraitser syndrome

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Jun 9, 2016
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000022914.10

Allele description [Variation Report for NM_003070.5(SMARCA2):c.3485G>A (p.Arg1162His)]

NM_003070.5(SMARCA2):c.3485G>A (p.Arg1162His)

Gene:

SMARCA2:SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p24.3

Genomic location:

Preferred name:

NM_003070.5(SMARCA2):c.3485G>A (p.Arg1162His)

HGVS:

NC_000009.12:g.2115850G>A
NG_032162.2:g.140561G>A
NM_001289396.2:c.3485G>A
NM_001289397.2:c.3311G>A
NM_003070.5:c.3485G>AMANE SELECT
NM_139045.4:c.3485G>A
NP_001276325.1:p.Arg1162His
NP_001276325.1:p.Arg1162His
NP_001276326.1:p.Arg1104His
NP_003061.3:p.Arg1162His
NP_620614.2:p.Arg1162His
LRG_882t1:c.3485G>A
LRG_882:g.140561G>A
LRG_882p1:p.Arg1162His
NC_000009.11:g.2115850G>A
NM_001289396.1:c.3485G>A
NM_003070.3:c.3485G>A
P51531:p.Arg1162His

Protein change:

R1104H; ARG1162HIS

Links:

UniProtKB: P51531#VAR_068203; UniProtKB/Swiss-Prot: VAR_068203; OMIM: 600014.0007; dbSNP: rs281875186

NCBI 1000 Genomes Browser:

rs281875186

Molecular consequence:

NM_001289396.2:c.3485G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001289397.2:c.3311G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003070.5:c.3485G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_139045.4:c.3485G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Nicolaides-Baraitser syndrome (NCBRS)
Synonyms:: Intellectual disability-sparse hair-brachydactyly syndrome
Identifiers:: MONDO: MONDO:0011053; MedGen: C1303073; Orphanet: 3051; OMIM: 601358

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000044205	OMIM	no assertion criteria provided	Pathogenic (Feb 26, 2012)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000291978	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha	criteria provided, single submitter (HA_assertions_20161101)	Pathogenic (Jun 9, 2016)	de novo	research	HA_assertions_20161101.pdf, Citation Link,
SCV001739361	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	de novo	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000044205

OMIM

no assertion criteria provided

Pathogenic
(Feb 26, 2012)

germline

literature only

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

SCV000291978

HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha

criteria provided, single submitter

(HA_assertions_20161101)

Pathogenic
(Jun 9, 2016)

de novo

research

HA_assertions_20161101.pdf,

Citation Link,

SCV001739361

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

de novo

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, research
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome.

Van Houdt JK, Nowakowska BA, Sousa SB, van Schaik BD, Seuntjens E, Avonce N, Sifrim A, Abdul-Rahman OA, van den Boogaard MJ, Bottani A, Castori M, Cormier-Daire V, Deardorff MA, Filges I, Fryer A, Fryns JP, Gana S, Garavelli L, Gillessen-Kaesbach G, Hall BD, Horn D, Huylebroeck D, et al.

Nat Genet. 2012 Feb 26;44(4):445-9, S1. doi: 10.1038/ng.1105.

PubMed [citation]

PMID:: 22366787

PMC

Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]

PMCID:: PMC4544753
PMID:: 25741868
DOI:: 10.1038/gim.2015.30

Details of each submission

From OMIM, SCV000044205.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In an individual with Nicolaides-Baraitser syndrome (NCBRS; 601358), Van Houdt et al. (2012) identified a de novo heterozygous G-to-A transition at nucleotide 3485 in exon 25 of the SMARCA2 gene, resulting in an arg-to-his substitution at codon 1162 (R1162H). This mutation was not seen in 1,300 control exomes.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-HudsonAlpha, SCV000291978.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV001739361.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		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	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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