NM_001130144.3:c.3900G>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001130144.3(LTBP3):c.3900G>A(p.Gln1300Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000783 in 1,276,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.8e-7 ( 0 hom. )
Consequence
LTBP3
NM_001130144.3 synonymous
NM_001130144.3 synonymous
Scores
1
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.51
Publications
0 publications found
Genes affected
LTBP3 (HGNC:6716): (latent transforming growth factor beta binding protein 3) The protein encoded by this gene forms a complex with transforming growth factor beta (TGF-beta) proteins and may be involved in their subcellular localization. Activation of this complex requires removal of the encoded binding protein. This protein also may play a structural role in the extracellular matrix. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]
LTBP3 Gene-Disease associations (from GenCC):
- brachyolmia-amelogenesis imperfecta syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- geleophysic dysplasia 3Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- Acromicric dysplasiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- geleophysic dysplasiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.154).
BP7
Synonymous conserved (PhyloP=1.51 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001130144.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LTBP3 | NM_001130144.3 | MANE Select | c.3900G>A | p.Gln1300Gln | synonymous | Exon 28 of 28 | NP_001123616.1 | Q9NS15-1 | |
| LTBP3 | NM_021070.4 | c.3759G>A | p.Gln1253Gln | synonymous | Exon 27 of 27 | NP_066548.2 | Q9NS15-2 | ||
| LTBP3 | NM_001164266.1 | c.3408G>A | p.Gln1136Gln | synonymous | Exon 27 of 27 | NP_001157738.1 | Q9NS15 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LTBP3 | ENST00000301873.11 | TSL:2 MANE Select | c.3900G>A | p.Gln1300Gln | synonymous | Exon 28 of 28 | ENSP00000301873.5 | Q9NS15-1 | |
| LTBP3 | ENST00000322147.8 | TSL:1 | c.3759G>A | p.Gln1253Gln | synonymous | Exon 27 of 27 | ENSP00000326647.4 | Q9NS15-2 | |
| LTBP3 | ENST00000528516.5 | TSL:1 | n.*3404G>A | non_coding_transcript_exon | Exon 27 of 27 | ENSP00000432350.1 | E9PRF2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 7.83e-7 AC: 1AN: 1276418Hom.: 0 Cov.: 31 AF XY: 0.00000160 AC XY: 1AN XY: 625542 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1276418
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
625542
show subpopulations
African (AFR)
AF:
AC:
0
AN:
25274
American (AMR)
AF:
AC:
0
AN:
22878
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21464
East Asian (EAS)
AF:
AC:
0
AN:
28392
South Asian (SAS)
AF:
AC:
0
AN:
69794
European-Finnish (FIN)
AF:
AC:
0
AN:
33412
Middle Eastern (MID)
AF:
AC:
0
AN:
3846
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1019478
Other (OTH)
AF:
AC:
0
AN:
51880
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Uncertain
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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