NM_003072.5(SMARCA4):c.2656A>G (p.Met886Val) AND Intellectual disability, autosomal dominant 16

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Feb 1, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV001810073.5

Allele description [Variation Report for NM_003072.5(SMARCA4):c.2656A>G (p.Met886Val)]

NM_003072.5(SMARCA4):c.2656A>G (p.Met886Val)

Gene:

SMARCA4:SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_003072.5(SMARCA4):c.2656A>G (p.Met886Val)

HGVS:

NC_000019.10:g.11021764A>G
NG_011556.3:g.65833A>G
NM_001128844.3:c.2656A>G
NM_001128845.2:c.2656A>G
NM_001128846.2:c.2656A>G
NM_001128847.4:c.2656A>G
NM_001128848.2:c.2656A>G
NM_001128849.3:c.2656A>G
NM_001374457.1:c.2656A>G
NM_001387283.1:c.2656A>G
NM_003072.5:c.2656A>GMANE SELECT
NP_001122316.1:p.Met886Val
NP_001122317.1:p.Met886Val
NP_001122318.1:p.Met886Val
NP_001122319.1:p.Met886Val
NP_001122320.1:p.Met886Val
NP_001122321.1:p.Met886Val
NP_001361386.1:p.Met886Val
NP_001374212.1:p.Met886Val
NP_003063.2:p.Met886Val
LRG_878t1:c.2656A>G
LRG_878:g.65833A>G
LRG_878p1:p.Met886Val
NC_000019.9:g.11132440A>G
NG_011556.2:g.65843A>G
NM_001128849.1:c.2656A>G
NM_003072.5:c.2656A>G
NR_164683.1:n.2946A>G

Protein change:

M886V

Links:

dbSNP: rs2146416371

NCBI 1000 Genomes Browser:

rs2146416371

Molecular consequence:

NM_001128844.3:c.2656A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001128845.2:c.2656A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001128846.2:c.2656A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001128847.4:c.2656A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001128848.2:c.2656A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001128849.3:c.2656A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374457.1:c.2656A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001387283.1:c.2656A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003072.5:c.2656A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_164683.1:n.2946A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Intellectual disability, autosomal dominant 16 (CSS4)
Synonyms:: COFFIN-SIRIS SYNDROME 4
Identifiers:: MONDO: MONDO:0013821; MedGen: C3553249; Orphanet: 1465; OMIM: 614609

Recent activity

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PREDICTED: Homo sapiens zinc finger CCCH-type containing 7A (ZC3H7A), transcript...
PREDICTED: Homo sapiens zinc finger CCCH-type containing 7A (ZC3H7A), transcript variant X2, mRNA
gi|767987144|ref|XM_006720877.2|

Nucleotide
PREDICTED: Rattus norvegicus adenosine deaminase-like (Adal), transcript variant...
PREDICTED: Rattus norvegicus adenosine deaminase-like (Adal), transcript variant X7, mRNA
gi|2678929304|ref|XM_063283715.1|

Nucleotide
adenosine deaminase-like protein isoform X2 [Rattus norvegicus]
adenosine deaminase-like protein isoform X2 [Rattus norvegicus]
gi|2678929305|ref|XP_063139785.1|

Protein
PREDICTED: Homo sapiens family with sequence similarity 120 member A (FAM120A), ...
PREDICTED: Homo sapiens family with sequence similarity 120 member A (FAM120A), transcript variant X3, mRNA
gi|2462623723|ref|XM_054362503.1|

Nucleotide
PREDICTED: Homo sapiens family with sequence similarity 120 member A (FAM120A), ...
PREDICTED: Homo sapiens family with sequence similarity 120 member A (FAM120A), transcript variant X4, mRNA
gi|2462623725|ref|XM_054362504.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002056182	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 15, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002515287	Daryl Scott Lab, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 1, 2022)	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 36474027

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002056182

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 15, 2021)

germline

clinical testing

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

SCV002515287

Daryl Scott Lab, Baylor College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 1, 2022)

de novo

clinical testing

PubMed (2)
[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	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

High molecular diagnostic yields and novel phenotypic expansions involving syndromic anorectal malformations.

Belanger Deloge R, Zhao X, Luna PN, Shaw CA, Rosenfeld JA, Scott DA.

Eur J Hum Genet. 2023 Mar;31(3):296-303. doi: 10.1038/s41431-022-01255-y. Epub 2022 Dec 6.

PubMed [citation]

PMID:: 36474027
PMCID:: PMC9995493

Details of each submission

From Genome-Nilou Lab, SCV002056182.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Daryl Scott Lab, Baylor College of Medicine, SCV002515287.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

#	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		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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