rs201835629

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_007283.7(MGLL):​c.412G>T​(p.Ala138Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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: 33)
Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

MGLL
NM_007283.7 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.256
Variant links:
Genes affected
MGLL (HGNC:17038): (monoglyceride lipase) This gene encodes a serine hydrolase of the AB hydrolase superfamily that catalyzes the conversion of monoacylglycerides to free fatty acids and glycerol. The encoded protein plays a critical role in several physiological processes including pain and nociperception through hydrolysis of the endocannabinoid 2-arachidonoylglycerol. Expression of this gene may play a role in cancer tumorigenesis and metastasis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.29215884).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MGLLNM_007283.7 linkc.412G>T p.Ala138Ser missense_variant Exon 5 of 8 ENST00000265052.10 NP_009214.1 Q99685A0A0C4DFN3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MGLLENST00000265052.10 linkc.412G>T p.Ala138Ser missense_variant Exon 5 of 8 1 NM_007283.7 ENSP00000265052.5 A0A0C4DFN3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000342
AC:
5
AN:
1461802
Hom.:
0
Cov.:
31
AF XY:
0.00000275
AC XY:
2
AN XY:
727200
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Uncertain
0.019
T
BayesDel_noAF
Benign
-0.21
CADD
Benign
0.30
DANN
Benign
0.49
DEOGEN2
Benign
0.090
.;.;T;T;T;.;.;T;T
Eigen
Benign
-1.0
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.27
N
LIST_S2
Benign
0.85
T;D;D;.;T;T;T;T;T
M_CAP
Benign
0.050
D
MetaRNN
Benign
0.29
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.70
T
MutationAssessor
Benign
0.68
.;.;N;N;.;.;.;.;.
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-1.0
N;N;N;N;N;N;.;N;N
REVEL
Uncertain
0.45
Sift
Benign
0.73
T;T;T;T;T;T;.;T;T
Sift4G
Benign
0.58
T;T;T;T;T;T;.;T;.
Polyphen
0.0050
.;.;B;B;.;B;.;.;.
Vest4
0.40
MutPred
0.73
.;.;Gain of glycosylation at T131 (P = 0.0341);Gain of glycosylation at T131 (P = 0.0341);.;.;Gain of glycosylation at T131 (P = 0.0341);.;.;
MVP
0.69
MPC
0.47
ClinPred
0.13
T
GERP RS
-7.9
Varity_R
0.073
gMVP
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: chr3-127439994; API