16-4340390-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_016069.11(PAM16):c.307G>A(p.Glu103Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,064 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 Uncertain significance (★).
Frequency
Consequence
NM_016069.11 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAM16 | NM_016069.11 | c.307G>A | p.Glu103Lys | missense_variant | Exon 5 of 5 | ENST00000318059.8 | NP_057153.8 | |
CORO7-PAM16 | NM_001201479.2 | c.3076G>A | p.Glu1026Lys | missense_variant | Exon 31 of 31 | NP_001188408.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAM16 | ENST00000318059.8 | c.307G>A | p.Glu103Lys | missense_variant | Exon 5 of 5 | 1 | NM_016069.11 | ENSP00000315693.3 | ||
CORO7-PAM16 | ENST00000572467.5 | c.3076G>A | p.Glu1026Lys | missense_variant | Exon 31 of 31 | 2 | ENSP00000460885.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248978Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135216
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460064Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 726328
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1517664). This variant has not been reported in the literature in individuals affected with PAM16-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.002%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 103 of the PAM16 protein (p.Glu103Lys). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at