NM_001130144.3(LTBP3):c.1936G>C (p.Gly646Arg) AND Brachyolmia-amelogenesis imperfecta syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 22, 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:: RCV003756599.3

Allele description [Variation Report for NM_001130144.3(LTBP3):c.1936G>C (p.Gly646Arg)]

NM_001130144.3(LTBP3):c.1936G>C (p.Gly646Arg)

Genes:

LOC130006032:ATAC-STARR-seq lymphoblastoid silent region 3535 [Gene]
LTBP3:latent transforming growth factor beta binding protein 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.1

Genomic location:

Preferred name:

NM_001130144.3(LTBP3):c.1936G>C (p.Gly646Arg)

HGVS:

NC_000011.10:g.65547732C>G
NG_016437.1:g.15497G>C
NG_185477.1:g.242C>G
NM_001130144.3:c.1936G>CMANE SELECT
NM_001164266.1:c.1585G>C
NM_021070.4:c.1936G>C
NP_001123616.1:p.Gly646Arg
NP_001157738.1:p.Gly529Arg
NP_066548.2:p.Gly646Arg
NC_000011.9:g.65315203C>G

Protein change:

G529R

Links:

dbSNP: rs2496154378

NCBI 1000 Genomes Browser:

rs2496154378

Molecular consequence:

NM_001130144.3:c.1936G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001164266.1:c.1585G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_021070.4:c.1936G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Brachyolmia-amelogenesis imperfecta syndrome
Synonyms:: PLATYSPONDYLY WITH AMELOGENESIS IMPERFECTA; Tooth agenesis, selective, 6; Dental anomalies and short stature
Identifiers:: MONDO: MONDO:0011018; MedGen: C1832594; Orphanet: 2899; OMIM: 601216

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004554787	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 22, 2023)	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

SCV004554787

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 22, 2023)

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	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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004554787.2

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

Description

An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with LTBP3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 646 of the LTBP3 protein (p.Gly646Arg).

#	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 16, 2025

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