rs1555971008

Variant names:

• chrX-38352582-C-T
• rs1555971008
• ENST00000465127.1:c.172-313539C>T

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 6P and 1B. PS3 PM2 BP4

The NM_001407092.1(OTC):​c.-79-36C>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 (★). ClinVar reports functional evidence for this variant: "SCV000612173: Functional testing in cultured cells indicates reduced expression of reporter gene.".

• Frequency: Genomes: not found (cov: 23)
• Consequence: OTC NM_001407092.1 intron
• Clinical Significance: Uncertain significance criteria provided, single submitter P:1 U:1
• Conservation: PhyloP100: 3.99
• Publications: 1 publications found

Genes affected

ENSG00000250349 (HGNC:):

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]

OTC Gene-Disease associations (from GenCC):

• ornithine carbamoyltransferase deficiency

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Laboratory for Molecular Medicine, ClinGen, G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 5 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV000612173: Functional testing in cultured cells indicates reduced expression of reporter gene.
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001407092.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OTC	NM_001407092.1		c.-79-36C>T		intron	N/A	NP_001394021.1	P00480
	OTC	NM_000531.6	MANE Select	c.-115C>T		upstream_gene	N/A	NP_000522.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250349	ENST00000465127.1	TSL:5	c.172-313539C>T		intron	N/A	ENSP00000417050.1	B4E171
	OTC	ENST00000909238.1		c.-115C>T		5_prime_UTR	Exon 1 of 10	ENSP00000579297.1
	OTC	ENST00000909239.1		c.-115C>T		5_prime_UTR	Exon 1 of 9	ENSP00000579298.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 6

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	1	-	Ornithine carbamoyltransferase deficiency (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	21
DANN	Benign	0.94
PhyloP100		4.0
PromoterAI		0.00030	Neutral
Mutation Taster		=101/199	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1555971008; hg19: chrX-38211835;