chr1-231241424-ACCAGTC-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_014236.4(GNPAT):c.51_56del(p.Pro18_Ser19del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Consequence
GNPAT
NM_014236.4 inframe_deletion
NM_014236.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.28
Genes affected
GNPAT (HGNC:4416): (glyceronephosphate O-acyltransferase) This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
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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_014236.4.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPAT | NM_014236.4 | c.51_56del | p.Pro18_Ser19del | inframe_deletion | 1/16 | ENST00000366647.9 | |
GNPAT | NM_001316350.2 | c.51_56del | p.Pro18_Ser19del | inframe_deletion | 1/15 | ||
GNPAT | XM_005273313.5 | c.51_56del | p.Pro18_Ser19del | inframe_deletion | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPAT | ENST00000366647.9 | c.51_56del | p.Pro18_Ser19del | inframe_deletion | 1/16 | 1 | NM_014236.4 | P1 | |
GNPAT | ENST00000416000.1 | c.51_56del | p.Pro18_Ser19del | inframe_deletion | 1/13 | 5 | |||
GNPAT | ENST00000436239.5 | c.51_56del | p.Pro18_Ser19del | inframe_deletion | 1/6 | 3 | |||
GNPAT | ENST00000644483.1 | c.51_56del | p.Pro18_Ser19del | inframe_deletion, NMD_transcript_variant | 1/17 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals with GNPAT-related conditions. This variant is not present in population databases (ExAC no frequency). This variant, c.51_56del, results in the deletion of 2 amino acid(s) of the GNPAT protein (p.Pro18_Ser19del), but otherwise preserves the integrity of the reading frame. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.