9-130494983-C-T

Position:

• chr9-130494983-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_054012.4(ASS1):​c.1087C>T​(p.Arg363Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000341 in 1,613,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R363L) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.000039 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000034 (0 hom.)
• Consequence: ASS1 NM_054012.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:13
• Conservation: PhyloP100: 3.90

Genes affected

ASS1 (HGNC:758): (argininosuccinate synthase 1) The protein encoded by this gene catalyzes the penultimate step of the arginine biosynthetic pathway. There are approximately 10 to 14 copies of this gene including the pseudogenes scattered across the human genome, among which the one located on chromosome 9 appears to be the only functional gene for argininosuccinate synthetase. Mutations in the chromosome 9 copy of this gene cause citrullinemia. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2012]

ASS1 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a strand (size 7) in uniprot entity ASSY_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_054012.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.985
• PP5: Variant 9-130494983-C-T is Pathogenic according to our data. Variant chr9-130494983-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 6328.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-130494983-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASS1	NM_054012.4	c.1087C>T	p.Arg363Trp	missense_variant	13/15	ENST00000352480.10	NP_446464.1
ASS1	NM_000050.4	c.1087C>T	p.Arg363Trp	missense_variant	14/16		NP_000041.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASS1	ENST00000352480.10	c.1087C>T	p.Arg363Trp	missense_variant	13/15	1	NM_054012.4	ENSP00000253004.6
ASS1	ENST00000372393.7	c.1087C>T	p.Arg363Trp	missense_variant	14/16	5		ENSP00000361469.2
ASS1	ENST00000372394.5	c.1087C>T	p.Arg363Trp	missense_variant	14/16	2		ENSP00000361471.1
ASS1	ENST00000372386.6	n.358C>T		non_coding_transcript_exon_variant	4/6	3

Frequencies

GnomAD3 genomes AF: 0.0000394 AC: 6 AN: 152136 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000320 AC: 8 AN: 250206 Hom.: 0 AF XY: 0.0000222 AC XY: 3 AN XY: 135400

Gnomad AFR exome AF: 0.0000618

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000529

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000335 AC: 49 AN: 1460994 Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20 AN XY: 726828

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000423

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.0000394 AC: 6 AN: 152136 Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6 AN XY: 74330

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000735

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000116 Hom.: 0

Bravo AF: 0.0000567

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:13

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Citrullinemia type I Pathogenic:8

Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Jun 03, 2020	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 04, 2013	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Nov 01, 2021	NM_000050.4(ASS1):c.1087C>T(R363W) is a missense variant classified as likely pathogenic in the context of citrullinemia type 1. R363W has been observed in cases with relevant disease (PMID: 16124451, 26117549, 2358466, 14680976, 25537548, 31056765, 30904546). Functional assessments of this variant are available in the literature (PMID: 31469252). Internal structural analysis of the variant is supportive of pathogenicity. R363W has been observed in population frequency databases (gnomAD: AFR 0.01%). In summary, NM_000050.4(ASS1):c.1087C>T(R363W) is a missense variant that has both functional and internal structural support for pathogenicity and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 20, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 26, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 04, 2019	The ASS1 c.1087C>T, p.Arg363Trp variant (rs121908640) is reported in the literature in multiple individuals affected with citrullinemia, either in a homozygous state or compound heterozygous with another pathogenic variant (Diez-Fernandez 2017, Faghfoury 2011, Gao 2003, Haberle 2003, Kobayashi 1990, Mohamed 2015, Wasant 2005). This variant is reported as pathogenic or likely pathogenic by multiple laboratories in ClinVar (Variation ID: 6328), and is only observed on 8 alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. The arginine at codon 363 is moderately conserved, and computational analyses (SIFT: damaging, PolyPhen-2: benign) predict conflicting effects of this variant on protein structure/function. However, arginine 363 is implicated in tetramer binding, which is critical for protein function (Diez-Fernandez 2017). Additionally, other amino acid substitutions at this codon (Gly, Leu, Gln) have been reported in individuals with citrullinemia (Gao 2003, Mohamed 2015). Based on available information, the p.Arg363Trp variant is considered to be pathogenic. References: Diez-Fernandez C et al. Mutations in the Human Argininosuccinate Synthetase (ASS1) Gene, Impact on Patients, Common Changes, and Structural Considerations. Hum Mutat. 2017 May;38(5):471-484. Faghfoury H et al. Transient fulminant liver failure as an initial presentation in citrullinemia type I. Mol Genet Metab. 2011; 102(4):413-7. Gao H et al. Identification of 16 novel mutations in the argininosuccinate synthetase gene and genotype-phenotype correlation in 38 classical citrullinemia patients. Hum Mutat. 2003; 22(1):24-34. Haberle J et al. Mild citrullinemia in Caucasians is an allelic variant of argininosuccinate synthetase deficiency (citrullinemia type 1). Mol Genet Metab. 2003 Nov;80(3):302-6. Kobayashi K et al. Heterogeneity of mutations in argininosuccinate synthetase causing human citrullinemia. J Biol Chem. 1990; 265(19):11361-7. Mohamed S et al. Neurometabolic Disorders-Related Early Childhood Epilepsy: A Single-Center Experience in Saudi Arabia. Pediatr Neonatol. 2015 Dec;56(6):393-401. Wasant P et al. Argininosuccinate synthetase deficiency: mutation analysis in 3 Thai patients. Southeast Asian J Trop Med Public Health. 2005; 36(3):757-61. -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Sep 22, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 31, 2018	- -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Jun 30, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2025	Published functional studies demonstrate reduced enzyme activity (PMID: 31469252); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31208364, 14680976, 21227727, 26117549, 16124451, 28750687, 28111830, 28132756, 2358466, 25537548, 8792870, 32778825, 12815590, 31469252, 37485339, 37308883, 6819208, 35095998, 35726796) -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Apr 25, 2018	- -

Citrullinemia Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 30, 2021	Variant summary: ASS1 c.1087C>T (p.Arg363Trp) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 250206 control chromosomes (gnomAD). c.1087C>T has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with Citrullinemia Type I (e.g. Haberle_2003, Wasant_2005, Zielonka_2019). These data indicate that the variant is very likely to be associated with disease. At least one publication reported experimental evidence evaluating an impact on protein function, and demonstrated severely diminished activity compared to the wild type (Zielonka_2019). Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, and all laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 25, 2024	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 363 of the ASS1 protein (p.Arg363Trp). This variant is present in population databases (rs121908640, gnomAD 0.007%). This missense change has been observed in individual(s) with citrullinemia type 1 (PMID: 2358466, 12815590, 14680976, 16124451, 25537548, 26117549, 28111830). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 6328). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ASS1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects ASS1 function (PMID: 8792870). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.55
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	1.0	D;D;D
Eigen	Uncertain	0.63
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Uncertain	0.92	.;.;D
M_CAP	Pathogenic	0.64	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.2	H;H;H
PrimateAI	Uncertain	0.73	T
PROVEAN	Pathogenic	-7.8	D;D;D
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;D;D
Sift4G	Uncertain	0.024	D;D;D
Polyphen		0.83	P;P;P
Vest4		0.99
MVP		0.99
MPC		0.48
ClinPred		1.0	D
GERP RS		3.7
Varity_R		0.93
gMVP		0.91

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs121908640; hg19: chr9-133370370;