chr9-127695053-TTGATGATGATGATGATGATGATGA-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The ENST00000335223.5(PTRH1):c.270_293delTCATCATCATCATCATCATCATCA(p.His90_His97del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000625 in 671,816 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000044 ( 0 hom. )
Consequence
PTRH1
ENST00000335223.5 disruptive_inframe_deletion
ENST00000335223.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.09
Genes affected
PTRH1 (HGNC:27039): (peptidyl-tRNA hydrolase 1 homolog) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]
STXBP1 (HGNC:11444): (syntaxin binding protein 1) This gene encodes a syntaxin-binding protein. The encoded protein appears to play a role in release of neurotransmitters via regulation of syntaxin, a transmembrane attachment protein receptor. Mutations in this gene have been associated with infantile epileptic encephalopathy-4. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in ENST00000335223.5
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PTRH1 | XM_047422774.1 | c.527_550delTCATCATCATCATCATCATCATCA | p.Ile176_Ile183del | disruptive_inframe_deletion | Exon 5 of 5 | XP_047278730.1 | ||
| PTRH1 | XM_047422775.1 | c.371_394delTCATCATCATCATCATCATCATCA | p.Ile124_Ile131del | disruptive_inframe_deletion | Exon 4 of 4 | XP_047278731.1 | ||
| STXBP1 | NM_001374314.1 | c.*55_*78delATGATGATGATGATGATGATGATG | 3_prime_UTR_variant | Exon 19 of 19 | NP_001361243.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PTRH1 | ENST00000335223.5 | c.270_293delTCATCATCATCATCATCATCATCA | p.His90_His97del | disruptive_inframe_deletion | Exon 2 of 3 | 1 | ENSP00000493136.1 | |||
| STXBP1 | ENST00000636962.2 | c.*55_*78delATGATGATGATGATGATGATGATG | 3_prime_UTR_variant | Exon 19 of 19 | 5 | ENSP00000489762.1 | ||||
| STXBP1 | ENST00000635950.2 | n.*55_*78delATGATGATGATGATGATGATGATG | non_coding_transcript_exon_variant | Exon 19 of 20 | 5 | ENSP00000490903.1 |
Frequencies
GnomAD3 genomes 0.000129 AC: 19AN: 147598Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000439 AC: 23AN: 524098Hom.: 0 AF XY: 0.0000529 AC XY: 15AN XY: 283540
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GnomAD4 genome 0.000129 AC: 19AN: 147718Hom.: 0 Cov.: 0 AF XY: 0.0000975 AC XY: 7AN XY: 71782
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at