19-7535563-CT-GG
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_001166111.2(PNPLA6):c.13_14delCTinsGG(p.Leu5Gly) variant causes a missense 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
Consequence
NM_001166111.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PNPLA6 | NM_001166111.2 | c.13_14delCTinsGG | p.Leu5Gly | missense_variant | NP_001159583.1 | |||
PNPLA6 | NM_001166113.1 | c.13_14delCTinsGG | p.Leu5Gly | missense_variant | NP_001159585.1 | |||
PNPLA6 | NM_006702.5 | c.13_14delCTinsGG | p.Leu5Gly | missense_variant | NP_006693.3 | |||
PNPLA6 | NM_001166112.2 | c.13_14delCTinsGG | p.Leu5Gly | missense_variant | NP_001159584.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000268614 | ENST00000601870.1 | n.*426_*427delCTinsGG | non_coding_transcript_exon_variant | Exon 6 of 10 | 4 | ENSP00000471492.1 | ||||
ENSG00000268614 | ENST00000601870.1 | n.*426_*427delCTinsGG | 3_prime_UTR_variant | Exon 6 of 10 | 4 | ENSP00000471492.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 39 Uncertain:1
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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). ClinVar contains an entry for this variant (Variation ID: 843409). This variant has not been reported in the literature in individuals affected with PNPLA6-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.09%). This sequence change replaces leucine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 5 of the PNPLA6 protein (p.Leu5Gly). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at