1-227733461-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_023007.3(JMJD4):c.775G>A(p.Glu259Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000151 in 1,589,696 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_023007.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JMJD4 | ENST00000620518.5 | c.775G>A | p.Glu259Lys | missense_variant | Exon 4 of 6 | 1 | NM_023007.3 | ENSP00000477669.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000433 AC: 1AN: 231202Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 125682
GnomAD4 exome AF: 0.0000104 AC: 15AN: 1437482Hom.: 0 Cov.: 32 AF XY: 0.0000112 AC XY: 8AN XY: 713098
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.913G>A (p.E305K) alteration is located in exon 4 (coding exon 4) of the JMJD4 gene. This alteration results from a G to A substitution at nucleotide position 913, causing the glutamic acid (E) at amino acid position 305 to be replaced by a lysine (K). 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