rs66737144

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The NM_000531.6(OTC):​c.386+1G>A variant causes a splice donor, intron 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. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 23)

Consequence

OTC
NM_000531.6 splice_donor, intron

Scores

3
1
1
Splicing: ADA: 1.000
2

Clinical Significance

Pathogenic criteria provided, single submitter P:2

Conservation

PhyloP100: 7.34
Variant links:
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 Pathogenic. Variant got 12 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-38381430-G-A is Pathogenic according to our data. Variant chrX-38381430-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 97178.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OTCNM_000531.6 linkc.386+1G>A splice_donor_variant, intron_variant Intron 4 of 9 ENST00000039007.5 NP_000522.3 P00480
OTCNM_001407092.1 linkc.386+1G>A splice_donor_variant, intron_variant Intron 6 of 11 NP_001394021.1
OTCXM_017029556.2 linkc.386+1G>A splice_donor_variant, intron_variant Intron 4 of 8 XP_016885045.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OTCENST00000039007.5 linkc.386+1G>A splice_donor_variant, intron_variant Intron 4 of 9 1 NM_000531.6 ENSP00000039007.4 P00480
ENSG00000250349ENST00000465127.1 linkc.172-284691G>A intron_variant Intron 3 of 8 5 ENSP00000417050.1 B4E171
OTCENST00000488812.1 linkn.423+1G>A splice_donor_variant, intron_variant Intron 4 of 5 5
OTCENST00000643344.1 linkn.*136+1G>A splice_donor_variant, intron_variant Intron 5 of 10 ENSP00000496606.1 A0A2R8Y829

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
Cov.:
23
GnomAD4 genome
Cov.:
23

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Pathogenic:2
Mar 01, 2022
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate skipping of exon 4 in a majority of transcripts (Sacchetto et al., 2021); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 16786505, 34906067) -

-
GenMed Metabolism Lab
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.74
D
BayesDel_noAF
Pathogenic
0.37
CADD
Pathogenic
33
DANN
Uncertain
1.0
FATHMM_MKL
Pathogenic
0.97
D
GERP RS
5.9

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.92
SpliceAI score (max)
0.95
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.33
Position offset: 3
DS_DL_spliceai
0.95
Position offset: -1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs66737144; hg19: chrX-38240683; API