chr3-86968640-C-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_016206.4(VGLL3):c.887G>T(p.Gly296Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
VGLL3
NM_016206.4 missense
NM_016206.4 missense
Scores
6
9
4
Clinical Significance
Conservation
PhyloP100: 4.34
Genes affected
VGLL3 (HGNC:24327): (vestigial like family member 3) Predicted to enable protein C-terminus binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.836
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VGLL3 | NM_016206.4 | c.887G>T | p.Gly296Val | missense_variant | 3/4 | ENST00000398399.7 | NP_057290.2 | |
VGLL3 | NM_001320493.2 | c.887G>T | p.Gly296Val | missense_variant | 3/4 | NP_001307422.1 | ||
VGLL3 | NM_001320494.2 | c.728G>T | p.Gly243Val | missense_variant | 3/4 | NP_001307423.1 | ||
VGLL3 | XM_006713138.5 | c.884G>T | p.Gly295Val | missense_variant | 3/4 | XP_006713201.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VGLL3 | ENST00000398399.7 | c.887G>T | p.Gly296Val | missense_variant | 3/4 | 1 | NM_016206.4 | ENSP00000381436 | P1 | |
VGLL3 | ENST00000383698.3 | c.887G>T | p.Gly296Val | missense_variant | 3/4 | 1 | ENSP00000373199 | |||
VGLL3 | ENST00000637106.1 | upstream_gene_variant | 5 | ENSP00000489678 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.887G>T (p.G296V) alteration is located in exon 3 (coding exon 3) of the VGLL3 gene. This alteration results from a G to T substitution at nucleotide position 887, causing the glycine (G) at amino acid position 296 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Loss of glycosylation at T291 (P = 0.029);Loss of glycosylation at T291 (P = 0.029);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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
No publications associated with this variant yet.