rs746506861

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001042545.2(LTBP4):​c.211C>G​(p.Pro71Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000797 in 1,255,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict 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: 30)
Exomes š‘“: 8.0e-7 ( 0 hom. )

Consequence

LTBP4
NM_001042545.2 missense

Scores

1
2
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.336
Variant links:
Genes affected
LTBP4 (HGNC:6717): (latent transforming growth factor beta binding protein 4) The protein encoded by this gene binds transforming growth factor beta (TGFB) as it is secreted and targeted to the extracellular matrix. TGFB is biologically latent after secretion and insertion into the extracellular matrix, and sheds TGFB and other proteins upon activation. Defects in this gene may be a cause of cutis laxa and severe pulmonary, gastrointestinal, and urinary abnormalities. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.25116092).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LTBP4NM_001042545.2 linkc.211C>G p.Pro71Ala missense_variant Exon 1 of 30 ENST00000396819.8 NP_001036010.1 Q8N2S1-2B3KXY6
LTBP4NM_001042544.1 linkc.451+1421C>G intron_variant Intron 4 of 32 NP_001036009.1 Q8N2S1-1B3KXY6
LTBP4NM_003573.2 linkc.340+1421C>G intron_variant Intron 4 of 32 NP_003564.2 Q8N2S1A0A0C4DH07B3KXY6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LTBP4ENST00000396819.8 linkc.211C>G p.Pro71Ala missense_variant Exon 1 of 30 1 NM_001042545.2 ENSP00000380031.5 Q8N2S1-2

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
7.97e-7
AC:
1
AN:
1255178
Hom.:
0
Cov.:
31
AF XY:
0.00000163
AC XY:
1
AN XY:
614170
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000167
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.056
T
BayesDel_noAF
Benign
-0.32
CADD
Uncertain
23
DANN
Uncertain
0.99
Eigen
Benign
-0.036
Eigen_PC
Benign
0.00073
FATHMM_MKL
Uncertain
0.78
D
LIST_S2
Benign
0.50
T
M_CAP
Pathogenic
0.76
D
MetaRNN
Benign
0.25
T
MetaSVM
Benign
-0.65
T
PROVEAN
Benign
-0.010
N
REVEL
Benign
0.18
Sift
Benign
0.46
T
Sift4G
Benign
0.73
T
Vest4
0.27
MutPred
0.31
Gain of catalytic residue at P71 (P = 0.0301);
MVP
0.53
ClinPred
0.41
T
GERP RS
2.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-41107504; API