18-36122222-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012319.4(SLC39A6):c.1189G>A(p.Glu397Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012319.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A6 | ENST00000269187.10 | c.1189G>A | p.Glu397Lys | missense_variant | Exon 5 of 10 | 2 | NM_012319.4 | ENSP00000269187.4 | ||
SLC39A6 | ENST00000440549.6 | c.364G>A | p.Glu122Lys | missense_variant | Exon 4 of 8 | 1 | ENSP00000401139.1 | |||
SLC39A6 | ENST00000590986.5 | c.1189G>A | p.Glu397Lys | missense_variant | Exon 5 of 10 | 5 | ENSP00000465915.1 | |||
SLC39A6 | ENST00000586829.1 | c.-111G>A | upstream_gene_variant | 3 | ENSP00000467724.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249214Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135212
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727208
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1189G>A (p.E397K) alteration is located in exon 5 (coding exon 4) of the SLC39A6 gene. This alteration results from a G to A substitution at nucleotide position 1189, causing the glutamic acid (E) at amino acid position 397 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