X-38352581-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001407092.1(OTC):​c.-79-37C>T variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 22)

Consequence

OTC
NM_001407092.1 intron

Scores

2

Clinical Significance

Uncertain significance criteria provided, single submitter P:1U:1

Conservation

PhyloP100: 3.99
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 Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.17).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OTCNM_001407092.1 linkc.-79-37C>T intron_variant Intron 2 of 11 NP_001394021.1
OTCNM_000531.6 linkc.-116C>T upstream_gene_variant ENST00000039007.5 NP_000522.3 P00480
OTCXM_017029556.2 linkc.-116C>T upstream_gene_variant XP_016885045.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000250349ENST00000465127.1 linkc.172-313540C>T intron_variant Intron 3 of 8 5 ENSP00000417050.1 B4E171
OTCENST00000039007.5 linkc.-116C>T upstream_gene_variant 1 NM_000531.6 ENSP00000039007.4 P00480
OTCENST00000488812.1 linkn.-24C>T upstream_gene_variant 5
OTCENST00000643344.1 linkn.-116C>T upstream_gene_variant ENSP00000496606.1 A0A2R8Y829

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Cov.:
6
GnomAD4 genome
Cov.:
22

ClinVar

Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Ornithine carbamoyltransferase deficiency Pathogenic:1Uncertain:1
Jul 06, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant occurs in a non-coding region of the OTC gene. It does not change the encoded amino acid sequence of the OTC protein. This variant has been observed in individual(s) with clinical features of OTC deficiency (PMID: 29282796; Invitae). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Studies have shown that this variant alters OTC gene expression (PMID: 29282796). ClinVar contains an entry for this variant (Variation ID: 487343). -

Dec 12, 2017
Caldovic Lab, Children's National Health System
Significance: Likely pathogenic
Review Status: no assertion criteria provided
Collection Method: research

The patient had clinical and biochemical symptoms of OTC deficiency, and no disease causing sequence variants in the OTC coding sequence and canonical splice sites. Functional testing in cultured cells indicates reduced expression of reporter gene. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.17
CADD
Benign
23
DANN
Benign
0.94

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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: rs1555971006; hg19: chrX-38211834; API