chr12-27312632-T-G
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP2PP3_Strong
The NM_015000.4(STK38L):c.477T>G(p.Asp159Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,796 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_015000.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK38L | NM_015000.4 | c.477T>G | p.Asp159Glu | missense_variant | 6/14 | ENST00000389032.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK38L | ENST00000389032.8 | c.477T>G | p.Asp159Glu | missense_variant | 6/14 | 1 | NM_015000.4 | P1 | |
STK38L | ENST00000545470.5 | c.354T>G | p.Asp118Glu | missense_variant | 5/7 | 3 | |||
STK38L | ENST00000407753.2 | c.261-1872T>G | intron_variant, NMD_transcript_variant | 3 | |||||
STK38L | ENST00000544367.5 | c.*349T>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461796Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727190
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.477T>G (p.D159E) alteration is located in exon 6 (coding exon 5) of the STK38L gene. This alteration results from a T to G substitution at nucleotide position 477, causing the aspartic acid (D) at amino acid position 159 to be replaced by a glutamic acid (E). 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
Publications
No publications associated with this variant yet.