chr2-27496919-A-ACGGTTT
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_001486.4(GCKR):c.17_22dupGGTTTC(p.Arg6_Phe7dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0002 in 1,613,826 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001486.4 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GCKR | NM_001486.4 | c.17_22dupGGTTTC | p.Arg6_Phe7dup | disruptive_inframe_insertion | Exon 1 of 19 | ENST00000264717.7 | NP_001477.2 | |
GCKR | XM_011532763.1 | c.17_22dupGGTTTC | p.Arg6_Phe7dup | disruptive_inframe_insertion | Exon 1 of 13 | XP_011531065.1 | ||
GCKR | XR_001738699.1 | n.83_88dupGGTTTC | non_coding_transcript_exon_variant | Exon 1 of 13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GCKR | ENST00000264717.7 | c.17_22dupGGTTTC | p.Arg6_Phe7dup | disruptive_inframe_insertion | Exon 1 of 19 | 1 | NM_001486.4 | ENSP00000264717.2 | ||
GCKR | ENST00000472290.1 | n.39_44dupGGTTTC | non_coding_transcript_exon_variant | Exon 1 of 11 | 1 | |||||
GCKR | ENST00000417872.5 | n.74_79dupGGTTTC | non_coding_transcript_exon_variant | Exon 1 of 7 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251462Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135906
GnomAD4 exome AF: 0.000205 AC: 299AN: 1461600Hom.: 0 Cov.: 30 AF XY: 0.000204 AC XY: 148AN XY: 727144
GnomAD4 genome AF: 0.000151 AC: 23AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74426
ClinVar
Submissions by phenotype
not provided Uncertain:3
This variant, c.17_22dup, results in the insertion of 2 amino acid(s) of the GCKR protein (p.Arg6_Phe7dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs748731892, gnomAD 0.02%). This variant has been observed in individual(s) with hypertriglyceridemia (PMID: 20657596). ClinVar contains an entry for this variant (Variation ID: 1303199). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant does not substantially affect GCKR function (PMID: 24879641). 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. -
Identified in a patient with hypertriglyceridemia, reported as p.Q8_H9insRF due to the use of alternate nomenclature; however, specific clinical information was not provided (PMID: 20657596); In-frame insertion of 2 amino acids in a non-repeat region; One in vitro functional study suggests that this variant has a mild impact on protein function and does not affect protein expression (PMID: 24879641); This variant is associated with the following publications: (PMID: 20657596, 34426522, 24879641, 36325899) -
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Fasting plasma glucose level quantitative trait locus 5 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at