rs111060774
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP5
The NM_000531.6(OTC):c.717+8_717+23del variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 22)
Consequence
OTC
NM_000531.6 splice_donor_5th_base, intron
NM_000531.6 splice_donor_5th_base, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.87
Genes affected
OTC (HGNC:8512): (ornithine transcarbamylase) This nuclear gene encodes a mitochondrial matrix enzyme. The encoded protein is involved in the urea cycle which functions to detoxify ammonia into urea for excretion. Mutations in this enzyme lead to ornithine transcarbamylase deficiency, which causes hyperammonemia. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PP5
?
Variant X-38408799-TGCTCTTTACATGTAAA-T is Pathogenic according to our data. Variant chrX-38408799-TGCTCTTTACATGTAAA-T is described in ClinVar as [Pathogenic]. Clinvar id is 97300.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.717+8_717+23del | splice_donor_5th_base_variant, intron_variant | ENST00000039007.5 | |||
OTC | NM_001407092.1 | c.717+8_717+23del | splice_donor_5th_base_variant, intron_variant | ||||
OTC | XM_017029556.2 | c.717+8_717+23del | splice_donor_5th_base_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.717+8_717+23del | splice_donor_5th_base_variant, intron_variant | 1 | NM_000531.6 | P1 | |||
OTC | ENST00000643344.1 | c.*467+8_*467+23del | splice_donor_5th_base_variant, intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | GenMed Metabolism Lab | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at