rs142993240

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The ENST00000371696.7(AGPAT2):​c.475C>T​(p.Arg159Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00516 in 1,570,472 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R159L) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0045 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0052 ( 30 hom. )

Consequence

AGPAT2
ENST00000371696.7 missense

Scores

1
7
11

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:8O:1

Conservation

PhyloP100: 2.85
Variant links:
Genes affected
AGPAT2 (HGNC:325): (1-acylglycerol-3-phosphate O-acyltransferase 2) This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. The protein is located within the endoplasmic reticulum membrane and converts lysophosphatidic acid to phosphatidic acid, the second step in de novo phospholipid biosynthesis. Mutations in this gene have been associated with congenital generalized lipodystrophy (CGL), or Berardinelli-Seip syndrome, a disease characterized by a near absence of adipose tissue and severe insulin resistance. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.013234198).
BP6
Variant 9-136676978-G-A is Benign according to our data. Variant chr9-136676978-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 210105.We mark this variant Likely_benign, oryginal submissions are: {Benign=6, Likely_benign=1, Uncertain_significance=1, Uncertain_risk_allele=1}. Variant chr9-136676978-G-A is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00451 (671/148876) while in subpopulation SAS AF= 0.00814 (37/4548). AF 95% confidence interval is 0.00607. There are 6 homozygotes in gnomad4. There are 327 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
AGPAT2NM_006412.4 linkuse as main transcriptc.475C>T p.Arg159Cys missense_variant 3/6 ENST00000371696.7 NP_006403.2
AGPAT2NM_001012727.2 linkuse as main transcriptc.475C>T p.Arg159Cys missense_variant 3/5 NP_001012745.1
AGPAT2XM_047422636.1 linkuse as main transcriptc.166C>T p.Arg56Cys missense_variant 3/6 XP_047278592.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AGPAT2ENST00000371696.7 linkuse as main transcriptc.475C>T p.Arg159Cys missense_variant 3/61 NM_006412.4 ENSP00000360761 P1O15120-1
AGPAT2ENST00000371694.7 linkuse as main transcriptc.475C>T p.Arg159Cys missense_variant 3/51 ENSP00000360759 O15120-2
AGPAT2ENST00000472820.1 linkuse as main transcriptn.403C>T non_coding_transcript_exon_variant 1/41
AGPAT2ENST00000470861.1 linkuse as main transcript downstream_gene_variant 2

Frequencies

GnomAD3 genomes
AF:
0.00451
AC:
671
AN:
148742
Hom.:
6
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00141
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00568
Gnomad ASJ
AF:
0.0102
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00814
Gnomad FIN
AF:
0.00142
Gnomad MID
AF:
0.0255
Gnomad NFE
AF:
0.00621
Gnomad OTH
AF:
0.00824
GnomAD3 exomes
AF:
0.00514
AC:
1277
AN:
248240
Hom.:
9
AF XY:
0.00561
AC XY:
756
AN XY:
134796
show subpopulations
Gnomad AFR exome
AF:
0.000557
Gnomad AMR exome
AF:
0.00498
Gnomad ASJ exome
AF:
0.0101
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00715
Gnomad FIN exome
AF:
0.00134
Gnomad NFE exome
AF:
0.00624
Gnomad OTH exome
AF:
0.00918
GnomAD4 exome
AF:
0.00523
AC:
7438
AN:
1421596
Hom.:
30
Cov.:
38
AF XY:
0.00541
AC XY:
3823
AN XY:
706970
show subpopulations
Gnomad4 AFR exome
AF:
0.000897
Gnomad4 AMR exome
AF:
0.00525
Gnomad4 ASJ exome
AF:
0.0113
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00745
Gnomad4 FIN exome
AF:
0.00207
Gnomad4 NFE exome
AF:
0.00524
Gnomad4 OTH exome
AF:
0.00623
GnomAD4 genome
AF:
0.00451
AC:
671
AN:
148876
Hom.:
6
Cov.:
32
AF XY:
0.00450
AC XY:
327
AN XY:
72600
show subpopulations
Gnomad4 AFR
AF:
0.00140
Gnomad4 AMR
AF:
0.00567
Gnomad4 ASJ
AF:
0.0102
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00814
Gnomad4 FIN
AF:
0.00142
Gnomad4 NFE
AF:
0.00621
Gnomad4 OTH
AF:
0.00815
Alfa
AF:
0.00642
Hom.:
4
Bravo
AF:
0.00459
TwinsUK
AF:
0.00485
AC:
18
ALSPAC
AF:
0.00363
AC:
14
ESP6500AA
AF:
0.00136
AC:
6
ESP6500EA
AF:
0.00558
AC:
48
ExAC
AF:
0.00545
AC:
661
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:8Other:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Benign:3
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 18, 2024- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2023AGPAT2: BS2 -
Uncertain significance, criteria provided, single submitterclinical testingMayo Clinic Laboratories, Mayo ClinicDec 30, 2021- -
not specified Benign:2
Benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoNov 07, 2018- -
Benign, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpFeb 19, 2022Variant summary: AGPAT2 c.475C>T (p.Arg159Cys) results in a non-conservative amino acid change located in the Phospholipid/glycerol acyltransferase domain (IPR002123) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0051 in 248240 control chromosomes in the gnomAD database, including 9 homozygotes. The observed variant frequency is approximately 5.9 fold of the estimated maximal expected allele frequency for a pathogenic variant in AGPAT2 causing Congenital Generalized Lipodystrophy phenotype (0.00087), strongly suggesting that the variant is benign. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign. -
Congenital generalized lipodystrophy type 1 Benign:1Other:1
Uncertain risk allele, criteria provided, single submitterresearchClinical Genomics, Uppaluri K&H Personalized Medicine Clinic-Potent mutations in AGPAT2 gene are associated with Congenital generalized lipodystrophy, type 1, which can present with insulin resistance, fatty liver and diabetes. rs142993240 variant is prevalent with Congenital Generalized Lipoatrophy. However, the role of this rs142993240 particular variant is yet to be ascertained. -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaApr 27, 2017This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
AGPAT2-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMay 01, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Monogenic diabetes Benign:1
Benign, criteria provided, single submitterresearchPersonalized Diabetes Medicine Program, University of Maryland School of MedicineFeb 22, 2019ACMG criteria: BS1 (1% in gnomAD AJ population, 0.5% overall MAF in gnomAD; disease prevalence 1:10 million gives MAF of 0.03%), BS2 (8 homozygotes in gnomAD) [REVEL 0.582, BP4 (3 predictors), PP3 (6 predictors)= conflicting evidence, not using]; heterozygotes mutation found in brother and sister with lipodytrophy phenotype Simsir et al. 2015 ""Heterozygous AGPAT2 Mutation, Diabetes, and Lipodystrophy in Extremities"" (no PMID)= benign -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.12
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.63
.;D;D
Eigen
Uncertain
0.39
Eigen_PC
Uncertain
0.28
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Benign
0.84
T;.;T
M_CAP
Pathogenic
0.38
D
MetaRNN
Benign
0.013
T;T;T
MetaSVM
Uncertain
0.56
D
MutationAssessor
Benign
1.9
L;L;L
MutationTaster
Benign
0.98
D;D;D
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-1.3
N;N;N
REVEL
Uncertain
0.58
Sift
Benign
0.040
D;T;T
Sift4G
Benign
0.13
T;T;T
Polyphen
0.99
D;D;D
Vest4
0.33
MVP
0.99
MPC
0.68
ClinPred
0.015
T
GERP RS
2.7
Varity_R
0.28
gMVP
0.55

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs142993240; hg19: chr9-139571430; COSMIC: COSV58246892; COSMIC: COSV58246892; API