Genetic Variant CPS1:p.Met1? (chr2-210477765-T-G) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000430249.7(CPS1):c.2T>G(p.Met1?) variant causes a start lost, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

CPS1
ENST00000430249.7 start_lost, splice_region

Scores

Splicing: ADA: 0.0005495

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -0.170

Variant links:

Genes affected

CPS1 (HGNC:2323): (carbamoyl-phosphate synthase 1) The mitochondrial enzyme encoded by this gene catalyzes synthesis of carbamoyl phosphate from ammonia and bicarbonate. This reaction is the first committed step of the urea cycle, which is important in the removal of excess urea from cells. The encoded protein may also represent a core mitochondrial nucleoid protein. Three transcript variants encoding different isoforms have been found for this gene. The shortest isoform may not be localized to the mitochondrion. Mutations in this gene have been associated with carbamoyl phosphate synthetase deficiency, susceptibility to persistent pulmonary hypertension, and susceptibility to venoocclusive disease after bone marrow transplantation.[provided by RefSeq, May 2010]

CPS1 links:

LANCL1 (HGNC:6508): (LanC like glutathione S-transferase 1) This gene encodes a loosely associated peripheral membrane protein related to the LanC family of bacterial membrane-associated proteins involved in the biosynthesis of antimicrobial peptides. This protein may play a role as a peptide-modifying enzyme component in eukaryotic cells. Previously considered a member of the G-protein-coupled receptor superfamily, this protein is now in the LanC family. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Nov 2008]

LANCL1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
CPS1	NM_001122633.3 link	c.-17T>G	splice_region_variant	Exon 1 of 39	NP_001116105.2	P31327-1Q6PEK7
CPS1	NM_001369257.1 link	c.-137T>G	splice_region_variant	Exon 1 of 40	NP_001356186.1
CPS1	NM_001122633.3 link	c.-17T>G	5_prime_UTR_variant	Exon 1 of 39	NP_001116105.2	P31327-1Q6PEK7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	Protein	UniProt
CPS1	ENST00000430249.7 link	c.2T>G	p.Met1?	start_lost, splice_region_variant	Exon 1 of 39	1	ENSP00000402608.2	P31327-3
CPS1	ENST00000673510.1 link	c.-137T>G		splice_region_variant	Exon 1 of 40		ENSP00000500537.1	P31327-1
CPS1	ENST00000673630.1 link	c.-251T>G		splice_region_variant	Exon 1 of 40		ENSP00000501073.1	P31327-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000205

AC:

AN:

1461230

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726882

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33476

American (AMR)

AF:

0.00

AC:

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26114

East Asian (EAS)

AF:

0.00

AC:

AN:

39696

South Asian (SAS)

AF:

0.00

AC:

AN:

86176

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53388

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00000270

AC:

AN:

1111550

Other (OTH)

AF:

0.00

AC:

AN:

60356

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Congenital hyperammonemia, type I

Uncertain:1

Dec 04, 2017

Counsyl

Significance:Uncertain significance

Review Status:no assertion criteria provided

Collection Method:clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.085

BayesDel_noAF

Benign

-0.12

CADD

Benign

3.3

(source)

DANN

Benign

0.78

DEOGEN2

Benign

0.0060

T;.

Eigen

Benign

0.014

Eigen_PC

Benign

-0.42

FATHMM_MKL

Benign

0.056

LIST_S2

Uncertain

0.90

D;D

M_CAP

Benign

0.014

MetaRNN

Pathogenic

0.93

D;D

MetaSVM

Uncertain

0.34

PhyloP100

-0.17

PROVEAN

Benign

-0.45

N;N

REVEL

Benign

0.23

Sift

Pathogenic

0.0

D;D

Vest4

0.22

MutPred

0.99

Gain of MoRF binding (P = 0.0526);Gain of MoRF binding (P = 0.0526);

MVP

0.95

ClinPred

0.037

GERP RS

-0.55

PromoterAI

0.0067

Neutral

(source)

gMVP

0.75

Mutation Taster

=163/37

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00055

dbscSNV1_RF

Benign

0.024

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

Publications

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2-210477765-T-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over