NM_012200.4(B3GAT3):c.150del (p.Ile51fs) AND Larsen-like syndrome, B3GAT3 type

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 8, 2023
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:: RCV003641847.1

Allele description

NM_012200.4(B3GAT3):c.150del (p.Ile51fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

11q12.3

Genomic location:

Preferred name:

NM_012200.4(B3GAT3):c.150del (p.Ile51fs)

HGVS:

NC_000011.10:g.62620605del
NG_031863.1:g.6572del
NM_001288721.2:c.129del
NM_001288722.2:c.150del
NM_001288723.2:c.150del
NM_012200.4:c.150delMANE SELECT
NP_001275650.1:p.Ile44fs
NP_001275651.1:p.Ile51fs
NP_001275652.1:p.Ile51fs
NP_036332.2:p.Ile51fs
NC_000011.9:g.62388076del
NC_000011.9:g.62388077del
NR_109991.2:n.179del

Protein change:

I44fs

Molecular consequence:

NM_001288721.2:c.129del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001288722.2:c.150del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001288723.2:c.150del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012200.4:c.150del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_109991.2:n.179del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV004502789	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 8, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25893793, 27871226, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004502789

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 8, 2023)

germline

clinical testing

PubMed (3)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Skeletal dysplasia in a consanguineous clan from the island of Nias/Indonesia is caused by a novel mutation in B3GAT3.

Budde BS, Mizumoto S, Kogawa R, Becker C, Altmüller J, Thiele H, Rüschendorf F, Toliat MR, Kaleschke G, Hämmerle JM, Höhne W, Sugahara K, Nürnberg P, Kennerknecht I.

Hum Genet. 2015 Jul;134(7):691-704. doi: 10.1007/s00439-015-1549-2. Epub 2015 Apr 19.

PubMed [citation]

PMID:: 25893793

Functional validation of novel compound heterozygous variants in B3GAT3 resulting in severe osteopenia and fractures: expanding the disease phenotype.

Job F, Mizumoto S, Smith L, Couser N, Brazil A, Saal H, Patterson M, Gibson MI, Soden S, Miller N, Thiffault I, Saunders C, Yamada S, Hoffmann K, Sugahara K, Farrow E.

BMC Med Genet. 2016 Nov 21;17(1):86.

PubMed [citation]

PMID:: 27871226
PMCID:: PMC5117547

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004502789.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with B3GAT3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ile51Phefs*50) in the B3GAT3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in B3GAT3 are known to be pathogenic (PMID: 25893793, 27871226).

#	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: Feb 28, 2024

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