rs1057517656
Positions:
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
NM_006412.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.78
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGPAT2 | NM_006412.4 | c.755_763delTGAGGACCA | p.Met252_Thr254del | disruptive_inframe_deletion | 6/6 | ENST00000371696.7 | NP_006403.2 | |
AGPAT2 | NM_001012727.2 | c.659_667delTGAGGACCA | p.Met220_Thr222del | disruptive_inframe_deletion | 5/5 | NP_001012745.1 | ||
AGPAT2 | XM_047422636.1 | c.446_454delTGAGGACCA | p.Met149_Thr151del | disruptive_inframe_deletion | 6/6 | XP_047278592.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGPAT2 | ENST00000371696.7 | c.755_763delTGAGGACCA | p.Met252_Thr254del | disruptive_inframe_deletion | 6/6 | 1 | NM_006412.4 | ENSP00000360761.2 | ||
AGPAT2 | ENST00000371694.7 | c.659_667delTGAGGACCA | p.Met220_Thr222del | disruptive_inframe_deletion | 5/5 | 1 | ENSP00000360759.3 | |||
AGPAT2 | ENST00000472820.1 | n.683_691delTGAGGACCA | non_coding_transcript_exon_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1454740Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 723282
GnomAD4 exome
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1
AN:
1454740
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1
AN XY:
723282
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GnomAD4 genome Cov.: 34
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
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
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Calibrated prediction
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at