chr9-136677118-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_006412.4(AGPAT2):c.335C>T(p.Pro112Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000178 in 1,460,758 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006412.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGPAT2 | NM_006412.4 | c.335C>T | p.Pro112Leu | missense_variant | Exon 3 of 6 | ENST00000371696.7 | NP_006403.2 | |
AGPAT2 | NM_001012727.2 | c.335C>T | p.Pro112Leu | missense_variant | Exon 3 of 5 | NP_001012745.1 | ||
AGPAT2 | XM_047422636.1 | c.26C>T | p.Pro9Leu | missense_variant | Exon 3 of 6 | XP_047278592.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGPAT2 | ENST00000371696.7 | c.335C>T | p.Pro112Leu | missense_variant | Exon 3 of 6 | 1 | NM_006412.4 | ENSP00000360761.2 | ||
AGPAT2 | ENST00000371694.7 | c.335C>T | p.Pro112Leu | missense_variant | Exon 3 of 5 | 1 | ENSP00000360759.3 | |||
AGPAT2 | ENST00000472820.1 | n.263C>T | non_coding_transcript_exon_variant | Exon 1 of 4 | 1 | |||||
AGPAT2 | ENST00000470861.1 | n.629C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247618Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134570
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460758Hom.: 0 Cov.: 37 AF XY: 0.0000110 AC XY: 8AN XY: 726672
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 19026526, 21744063, 32924125, 18640396) -
Congenital generalized lipodystrophy type 1 Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at