NM_005664.4:c.482dupC
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PVS1_StrongPP5BS2
The NM_005664.4(MKRN3):c.482dupC(p.Ala162GlyfsTer15) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,613,582 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005664.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MKRN3 | NM_005664.4 | c.482dupC | p.Ala162GlyfsTer15 | frameshift_variant | Exon 1 of 1 | ENST00000314520.6 | NP_005655.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152192Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461390Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 726996
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
MKRN3-related disorder Pathogenic:1
The MKRN3 c.482dupC variant is predicted to result in a frameshift and premature protein termination (p.Ala162Glyfs*15). This variant has been reported to be causative for central precocious puberty (Abreu et al. 2013. PubMed ID: 23738509; Macedo et al. 2014. PubMed ID: 24628548; Schreiner et al. 2014. PubMed ID: 25011910; Simon et al. 2016. PubMed ID: 26431553; Bessa et al. 2017. PubMed ID: 27225315). Please note that MKRN3 is a paternally expressed, imprinted gene located in the Prader-Willi syndrome critical region and all affected individuals inherited the pathogenic variants from their fathers. This variant is reported in 0.013% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/15-23811404-G-GC). Frameshift variants in MKRN3 are expected to be pathogenic. This variant is interpreted as pathogenic. -
Precocious puberty, central, 2 Pathogenic:1
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not provided Uncertain:1
Frameshift variant predicted to result in protein truncation, as the last 346 amino acids are replaced with 14 different amino acids, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (HGMD); Also known as c.475_476insC and c.482_483insC; This variant is associated with the following publications: (PMID: 30675365, 24628548, 26431553, 31589614, 33383582, 32676665, 23738509, 25011910) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at