chr16-68302421-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_032178.3(SLC7A6OS):c.759C>G(p.Tyr253Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
SLC7A6OS
NM_032178.3 stop_gained
NM_032178.3 stop_gained
Scores
2
4
1
Clinical Significance
Conservation
PhyloP100: 0.748
Genes affected
SLC7A6OS (HGNC:25807): (solute carrier family 7 member 6 opposite strand) Predicted to be involved in developmental process. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be located in cytoplasm and nucleus. Implicated in progressive myoclonus epilepsy. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Stoplost variant in NM_032178.3 Downstream stopcodon found after 7 codons.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC7A6OS | NM_032178.3 | c.759C>G | p.Tyr253Ter | stop_gained | 4/5 | ENST00000263997.11 | |
SLC7A6OS | XM_011523372.4 | c.*77C>G | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC7A6OS | ENST00000263997.11 | c.759C>G | p.Tyr253Ter | stop_gained | 4/5 | 1 | NM_032178.3 | P1 | |
SLC7A6OS | ENST00000561590.1 | c.285C>G | p.Tyr95Ter | stop_gained | 2/2 | 2 | |||
SLC7A6OS | ENST00000561933.1 | n.900C>G | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
SLC7A6OS | ENST00000568315.1 | c.*77C>G | 3_prime_UTR_variant, NMD_transcript_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Sep 01, 2023 | Variant summary: SLC7A6OS c.759C>G (p.Tyr253X) results in a premature termination codon and is predicted to cause a truncation of the encoded protein. Although the variant is not predicted to cause absence of the protein through nonsense mediated decay, the variant disrupts the last 57 amino acids in the protein sequence. The molecular mechanism of disease attributed to SLC7A6OS is currently unknown. The variant was absent in 251472 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.759C>G in individuals affected with Epilepsy, Progressive Myoclonic, 12 and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
D
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.