NM_001106.3(ACVR2B):c.119G>A (p.Arg40His) AND Heterotaxy, visceral, 4, autosomal

This record was updated by the submitter. Please see the current version.

Germline classification:: Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:: Dec 6, 2017
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:: RCV000007261.2

Allele description

NM_001106.3(ACVR2B):c.119G>A (p.Arg40His)

Gene:

ACVR2B:activin A receptor type 2B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_001106.3(ACVR2B):c.119G>A (p.Arg40His)

HGVS:

NC_000003.12:g.38477353G>A
NG_011791.1:g.28055G>A
NM_001106.3:c.119G>A
NP_001097.2:p.Arg40His
NC_000003.11:g.38518844G>A
Q13705:p.Arg40His

Protein change:

R40H; ARG40HIS

Links:

UniProtKB: Q13705#VAR_013281; OMIM: 602730.0001; dbSNP: rs121434437

GMAF:

0.0030(A), 121434437

NCBI 1000 Genomes Browser:

rs121434437

Allele Frequency:

0.00137(A), GO-ESP

Molecular consequence:

NM_001106.3:c.119G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Heterotaxy, visceral, 4, autosomal (HTX4)
Identifiers:: MedGen: C3151057; Orphanet: 450; OMIM: 613751

Recent activity

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Acinetobacter baumannii A118 contig1503_21, whole genome shotgun sequence
Acinetobacter baumannii A118 contig1503_21, whole genome shotgun sequence
gi|319920214|gb|AEOW01001604.1||gnl AEOW01|contig1503_21

Nucleotide
lysophosphatidic acid receptor 6 [Homo sapiens]
lysophosphatidic acid receptor 6 [Homo sapiens]
gi|241982706|ref|NP_001155969.1|

Protein
FT-like protein [Oryza sativa Japonica Group]
FT-like protein [Oryza sativa Japonica Group]
gi|159157535|dbj|BAF92712.1|

Protein
TDRKH [Carlito syrichta]
TDRKH [Carlito syrichta]
Gene ID:103263768

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000027457	OMIM	no assertion criteria provided	Pathogenic (Jan 1, 1999)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000770523	Invitae	criteria provided, single submitter (Nykamp K et al. (Genet Med 2017))	Benign (Dec 6, 2017)	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

SCV000027457

OMIM

no assertion criteria provided

Pathogenic
(Jan 1, 1999)

germline

literature only

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

SCV000770523

Invitae

criteria provided, single submitter

(Nykamp K et al. (Genet Med 2017))

Benign
(Dec 6, 2017)

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Left-right axis malformations associated with mutations in ACVR2B, the gene for human activin receptor type IIB.

Kosaki R, Gebbia M, Kosaki K, Lewin M, Bowers P, Towbin JA, Casey B.

Am J Med Genet. 1999 Jan 1;82(1):70-6.

PubMed [citation]

PMID:: 9916847

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 OMIM, SCV000027457.1

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

Description

In 2 unrelated patients with left-right axis malformations (613751), Kosaki et al. (1999) found a G-to-A transition at nucleotide 119 in exon 2 of the ACVR2B gene resulting in an arg40-to-his amino acid substitution. One of the patients had ventricular inversion (dextrocardia), but intact ventricular septum and normally related great arteries. The patient also had a right aortic arch and a right-sided spleen, as well as anomalies of the inferior and the superior vena cava. The second patient had a complete atrial ventricular canal defect with dextro-transposed great arteries and obstruction to pulmonary outflow. Pulmonary venous return was normal, but like the first patient, there was an interrupted inferior vena cava with azygous continuation. This patient also had polysplenia and midline liver. The mutation was not found in 100 randomly selected control individuals.

#	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 Invitae, SCV000770523.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 28, 2018

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