13-45194254-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198404.3(KCTD4):c.314G>A(p.Arg105Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,614,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198404.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KCTD4 | NM_198404.3 | c.314G>A | p.Arg105Gln | missense_variant | Exon 2 of 2 | ENST00000379108.2 | NP_940686.2 | |
GTF2F2 | NM_004128.3 | c.305-13170C>T | intron_variant | Intron 4 of 7 | ENST00000340473.8 | NP_004119.1 | ||
GTF2F2 | XM_011535052.4 | c.382+10776C>T | intron_variant | Intron 5 of 8 | XP_011533354.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KCTD4 | ENST00000379108.2 | c.314G>A | p.Arg105Gln | missense_variant | Exon 2 of 2 | 6 | NM_198404.3 | ENSP00000368402.1 | ||
GTF2F2 | ENST00000340473.8 | c.305-13170C>T | intron_variant | Intron 4 of 7 | 1 | NM_004128.3 | ENSP00000340823.6 | |||
GTF2F2 | ENST00000706694.1 | n.134-13170C>T | intron_variant | Intron 1 of 5 | ENSP00000516507.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250910Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135574
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461832Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727206
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.314G>A (p.R105Q) alteration is located in exon 2 (coding exon 1) of the KCTD4 gene. This alteration results from a G to A substitution at nucleotide position 314, causing the arginine (R) at amino acid position 105 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at