NM_000531.6:c.77+3_77+6delAAGT

Variant names:

• chrX-38352773-GGTAA-G
• rs72558496
• NM_000531.6:c.77+3_77+6delAAGT

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PP3_Moderate PP5

The NM_000531.6(OTC):​c.77+3_77+6delAAGT variant causes a splice region, intron change. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 22)
• Consequence: OTC NM_000531.6 splice_region, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 5.08

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]

ENSG00000250349 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant X-38352773-GGTAA-G is Pathogenic according to our data. Variant chrX-38352773-GGTAA-G is described in ClinVar as [Pathogenic]. Clinvar id is 97315.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-38352773-GGTAA-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OTC	NM_000531.6	c.77+3_77+6delAAGT		splice_region_variant, intron_variant	Intron 1 of 9	ENST00000039007.5	NP_000522.3
OTC	NM_001407092.1	c.77+3_77+6delAAGT		splice_region_variant, intron_variant	Intron 3 of 11		NP_001394021.1
OTC	XM_017029556.2	c.77+3_77+6delAAGT		splice_region_variant, intron_variant	Intron 1 of 8		XP_016885045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OTC	ENST00000039007.5	c.77+1_77+4delGTAA		splice_donor_variant, splice_region_variant, intron_variant	Intron 1 of 9	1	NM_000531.6	ENSP00000039007.4
ENSG00000250349	ENST00000465127.1	c.172-313347_172-313344delGTAA		intron_variant	Intron 3 of 8	5		ENSP00000417050.1
OTC	ENST00000488812.1	n.169+1_169+4delGTAA		splice_donor_variant, splice_region_variant, intron_variant	Intron 1 of 5	5
OTC	ENST00000643344.1	n.77+1_77+4delGTAA		splice_donor_variant, splice_region_variant, intron_variant	Intron 1 of 10			ENSP00000496606.1

Frequencies

GnomAD3 genomes Cov.: 22

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 22

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

not provided Pathogenic:1

-

GenMed Metabolism Lab

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.84		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.22		Position offset: -14
DS_DL_spliceai		0.84		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs72558496; hg19: chrX-38212026;