NM_012200.4(B3GAT3):c.619-12G>A AND Larsen-like syndrome, B3GAT3 type

Germline classification:: Likely benign (2 submissions)
Last evaluated:: May 18, 2022
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:: RCV002108865.6

Allele description [Variation Report for NM_012200.4(B3GAT3):c.619-12G>A]

NM_012200.4(B3GAT3):c.619-12G>A

Gene:

B3GAT3:beta-1,3-glucuronyltransferase 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q12.3

Genomic location:

Preferred name:

NM_012200.4(B3GAT3):c.619-12G>A

HGVS:

NC_000011.10:g.62616808C>T
NG_009845.1:g.9068C>T
NG_031863.1:g.10368G>A
NM_001288721.2:c.598-12G>A
NM_001288722.2:c.619-12G>A
NM_001288723.2:c.619-12G>A
NM_012200.4:c.619-12G>AMANE SELECT
NC_000011.9:g.62384280C>T

Links:

dbSNP: rs372473452

NCBI 1000 Genomes Browser:

rs372473452

Molecular consequence:

NM_001288721.2:c.598-12G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001288722.2:c.619-12G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001288723.2:c.619-12G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_012200.4:c.619-12G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Larsen-like syndrome, B3GAT3 type
Synonyms:: LARSEN SYNDROME, AUTOSOMAL RECESSIVE; Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects; MULTIPLE JOINT DISLOCATIONS, SHORT STATURE, AND CRANIOFACIAL DYSMORPHISM WITH OR WITHOUT CONGENITAL HEART DEFECTS
Identifiers:: MONDO: MONDO:0009511; MedGen: C3278404; Orphanet: 284139; OMIM: 245600

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002437497	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Sep 10, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002795872	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (May 18, 2022)	unknown	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

SCV002437497

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Sep 10, 2021)

germline

clinical testing

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

SCV002795872

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(May 18, 2022)

unknown

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
not provided	unknown	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

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

Details of each submission

From Invitae, SCV002437497.3

#	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 Fulgent Genetics, Fulgent Genetics, SCV002795872.1

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

Last Updated: Feb 28, 2024

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