1-151365622-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate
The NM_003944.4(SELENBP1):c.985C>T(p.His329Tyr) variant causes a missense change involving the alteration of a 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 Likely pathogenic (★).
Frequency
Consequence
NM_003944.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SELENBP1 | NM_003944.4 | c.985C>T | p.His329Tyr | missense_variant | Exon 9 of 12 | ENST00000368868.10 | NP_003935.2 | |
SELENBP1 | NM_001258289.2 | c.1111C>T | p.His371Tyr | missense_variant | Exon 9 of 12 | NP_001245218.1 | ||
SELENBP1 | NM_001258288.2 | c.799C>T | p.His267Tyr | missense_variant | Exon 8 of 11 | NP_001245217.1 | ||
SELENBP1 | XM_047433576.1 | c.932C>T | p.Ala311Val | missense_variant | Exon 8 of 9 | XP_047289532.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Extra oral halitosis Pathogenic:1
This variant is interpreted as a Likely Pathogenic, for Extraoral halitosis, Autosomal Recessive inheritance. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS3 => Well-established functional studies show a deleterious effect (PMID:29255262). -
Extraoral halitosis due to methanethiol oxidase deficiency Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at