GeneBe

rs1057517656

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_006412.4(AGPAT2):​c.755_763delTGAGGACCA​(p.Met252_Thr254del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000000687 in 1,454,740 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

AGPAT2
NM_006412.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 6.78
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 Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_006412.4.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AGPAT2NM_006412.4 linkc.755_763delTGAGGACCA p.Met252_Thr254del disruptive_inframe_deletion Exon 6 of 6 ENST00000371696.7 NP_006403.2 O15120-1A0A024R8I7
AGPAT2NM_001012727.2 linkc.659_667delTGAGGACCA p.Met220_Thr222del disruptive_inframe_deletion Exon 5 of 5 NP_001012745.1 O15120-2A0A024R8F9
AGPAT2XM_047422636.1 linkc.446_454delTGAGGACCA p.Met149_Thr151del disruptive_inframe_deletion Exon 6 of 6 XP_047278592.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AGPAT2ENST00000371696.7 linkc.755_763delTGAGGACCA p.Met252_Thr254del disruptive_inframe_deletion Exon 6 of 6 1 NM_006412.4 ENSP00000360761.2 O15120-1
AGPAT2ENST00000371694.7 linkc.659_667delTGAGGACCA p.Met220_Thr222del disruptive_inframe_deletion Exon 5 of 5 1 ENSP00000360759.3 O15120-2
AGPAT2ENST00000472820.1 linkn.683_691delTGAGGACCA non_coding_transcript_exon_variant Exon 4 of 4 1

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
6.87e-7
AC:
1
AN:
1454740
Hom.:
0
AF XY:
0.00000138
AC XY:
1
AN XY:
723282
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:
0.0000118
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

Congenital generalized lipodystrophy type 1 Other:1
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GeneReviews
Significance: not provided
Review Status: no classification provided
Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs1057517656; hg19: chr9-139568277; API