NM_000531.6:c.1A>G

Variant names:

• chrX-38352697-A-G
• rs67752076
• NM_000531.6:c.1A>G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_Supporting PM2 PP5

The NM_000531.6(OTC):​c.1A>G​(p.Met1?) variant causes a start lost change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 23)
• Consequence: OTC NM_000531.6 start_lost
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 4.73

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 4 ACMG points.

• PVS1: Start lost variant, no pathogenic variants between lost start and next in-frame start position. Next in-frame start position is after 60 CDS bases. Genomic position: 38352756. Lost 0.056 part of the original CDS.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-38352697-A-G is Pathogenic according to our data. Variant chrX-38352697-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 97130.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OTC	NM_000531.6	c.1A>G	p.Met1?	start_lost	Exon 1 of 10	ENST00000039007.5	NP_000522.3
OTC	NM_001407092.1	c.1A>G	p.Met1?	start_lost	Exon 3 of 12		NP_001394021.1
OTC	XM_017029556.2	c.1A>G	p.Met1?	start_lost	Exon 1 of 9		XP_016885045.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OTC	ENST00000039007.5	c.1A>G	p.Met1?	start_lost	Exon 1 of 10	1	NM_000531.6	ENSP00000039007.4
ENSG00000250349	ENST00000465127.1	c.172-313424A>G		intron_variant	Intron 3 of 8	5		ENSP00000417050.1
OTC	ENST00000488812.1	n.93A>G		non_coding_transcript_exon_variant	Exon 1 of 6	5
OTC	ENST00000643344.1	n.1A>G		non_coding_transcript_exon_variant	Exon 1 of 11			ENSP00000496606.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 26

GnomAD4 genome Cov.: 23

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

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.64	D
BayesDel_noAF	Pathogenic	0.68
CADD	Benign	19
DANN	Uncertain	0.98
DEOGEN2	Benign	0.37	T
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.90	D
M_CAP	Pathogenic	1.0	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	0.86	D
PROVEAN	Benign	-0.58	N
REVEL	Uncertain	0.64
Sift	Benign	0.11	T
Sift4G	Benign	0.18	T
Polyphen		0.064	B
Vest4		0.96
MutPred		0.97		Loss of helix (P = 0.0626);
MVP		1.0
ClinPred		0.97	D
GERP RS		5.9
Varity_R		0.43
gMVP		0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs67752076; hg19: chrX-38211950;