chr4-83598671-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_032717.5(GPAT3):āc.1153A>Gā(p.Asn385Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000139 in 1,443,810 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 (ā ).
Frequency
Genomes: not found (cov: 28)
Exomes š: 0.0000014 ( 0 hom. )
Consequence
GPAT3
NM_032717.5 missense
NM_032717.5 missense
Scores
4
7
8
Clinical Significance
Conservation
PhyloP100: 9.13
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 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.835
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPAT3 | NM_032717.5 | c.1153A>G | p.Asn385Asp | missense_variant | 11/12 | ENST00000264409.5 | NP_116106.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPAT3 | ENST00000264409.5 | c.1153A>G | p.Asn385Asp | missense_variant | 11/12 | 1 | NM_032717.5 | ENSP00000264409.4 | ||
GPAT3 | ENST00000395226.6 | c.1153A>G | p.Asn385Asp | missense_variant | 12/13 | 1 | ENSP00000378651.2 | |||
GPAT3 | ENST00000611707.4 | c.1153A>G | p.Asn385Asp | missense_variant | 12/13 | 5 | ENSP00000482571.1 | |||
GPAT3 | ENST00000509044.1 | n.143A>G | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD3 genomes
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28
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250116Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135234
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GnomAD4 exome AF: 0.00000139 AC: 2AN: 1443810Hom.: 0 Cov.: 35 AF XY: 0.00000279 AC XY: 2AN XY: 717924
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GnomAD4 genome Cov.: 28
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28
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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 | Jan 10, 2023 | The c.1153A>G (p.N385D) alteration is located in exon 11 (coding exon 11) of the GPAT3 gene. This alteration results from a A to G substitution at nucleotide position 1153, causing the asparagine (N) at amino acid position 385 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;.
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;D;D
REVEL
Uncertain
Sift
Benign
.;D;D
Sift4G
Uncertain
T;T;T
Polyphen
D;D;D
Vest4
MVP
MPC
0.34
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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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