4-83598677-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_032717.5(GPAT3):c.1159G>T(p.Val387Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000284 in 1,406,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 27)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
GPAT3
NM_032717.5 missense
NM_032717.5 missense
Scores
10
5
1
Clinical Significance
Conservation
PhyloP100: 9.79
Genes affected
GPAT3 (HGNC:28157): (glycerol-3-phosphate acyltransferase 3) This gene encodes a member of the lysophosphatidic acid acyltransferase protein family. The encoded protein is an enzyme which catalyzes the conversion of glycerol-3-phosphate to lysophosphatidic acid in the synthesis of triacylglycerol. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.92
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPAT3 | NM_032717.5 | c.1159G>T | p.Val387Phe | missense_variant | 11/12 | ENST00000264409.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPAT3 | ENST00000264409.5 | c.1159G>T | p.Val387Phe | missense_variant | 11/12 | 1 | NM_032717.5 | P1 | |
GPAT3 | ENST00000395226.6 | c.1159G>T | p.Val387Phe | missense_variant | 12/13 | 1 | P1 | ||
GPAT3 | ENST00000611707.4 | c.1159G>T | p.Val387Phe | missense_variant | 12/13 | 5 | P1 | ||
GPAT3 | ENST00000509044.1 | n.149G>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 27
GnomAD3 genomes
Cov.:
27
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250246Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135306
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GnomAD4 exome AF: 0.00000284 AC: 4AN: 1406338Hom.: 0 Cov.: 35 AF XY: 0.00000143 AC XY: 1AN XY: 699022
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GnomAD4 genome Cov.: 27
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27
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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 | Feb 28, 2023 | The c.1159G>T (p.V387F) alteration is located in exon 11 (coding exon 11) of the GPAT3 gene. This alteration results from a G to T substitution at nucleotide position 1159, causing the valine (V) at amino acid position 387 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D;D;D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;.;.
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M;M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Pathogenic
D;D;D
Polyphen
D;D;D
Vest4
MutPred
Loss of stability (P = 0.1601);Loss of stability (P = 0.1601);Loss of stability (P = 0.1601);
MVP
MPC
0.40
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at