rs145138923

chr7-66081825-G-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PM5 PP5_Very_Strong

The NM_000048.4(ASL):c.35G>A(p.Arg12Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00183 in 1,613,768 control chromosomes in the GnomAD database, including 1 homozygotes. 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. R12L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0012 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0019 (1 hom.)
• Consequence: ASL NM_000048.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:23
• Conservation: PhyloP100: 8.84

Genes affected

ASL (HGNC:746): (argininosuccinate lyase) This gene encodes a member of the lyase 1 family. The encoded protein forms a cytosolic homotetramer and primarily catalyzes the reversible hydrolytic cleavage of argininosuccinate into arginine and fumarate, an essential step in the liver in detoxifying ammonia via the urea cycle. Mutations in this gene result in the autosomal recessive disorder argininosuccinic aciduria, or argininosuccinic acid lyase deficiency. A nontranscribed pseudogene is also located on the long arm of chromosome 22. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr7-66081824-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1518921.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP5: Variant 7-66081825-G-A is Pathogenic according to our data. Variant chr7-66081825-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 92360.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-66081825-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASL	NM_000048.4	c.35G>A	p.Arg12Gln	missense_variant	3/17	ENST00000304874.14
ASL	NM_001024943.2	c.35G>A	p.Arg12Gln	missense_variant	2/16
ASL	NM_001024944.2	c.35G>A	p.Arg12Gln	missense_variant	2/15
ASL	NM_001024946.2	c.35G>A	p.Arg12Gln	missense_variant	2/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASL	ENST00000304874.14	c.35G>A	p.Arg12Gln	missense_variant	3/17	1	NM_000048.4	P1

Frequencies

GnomAD3 genomes AF: 0.00116 AC: 177 AN: 152144 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000628

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000942

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00193

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.00113 AC: 284 AN: 250818 Hom.: 1 AF XY: 0.00122 AC XY: 166 AN XY: 135706

Gnomad AFR exome AF: 0.000555

Gnomad AMR exome AF: 0.000376

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00129

Gnomad NFE exome AF: 0.00195

Gnomad OTH exome AF: 0.00212

GnomAD4 exome AF: 0.00190 AC: 2779 AN: 1461506 Hom.: 1 Cov.: 31 AF XY: 0.00177 AC XY: 1286 AN XY: 727018

Gnomad4 AFR exome AF: 0.000418

Gnomad4 AMR exome AF: 0.000403

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00137

Gnomad4 NFE exome AF: 0.00232

Gnomad4 OTH exome AF: 0.00149

GnomAD4 genome AF: 0.00116 AC: 177 AN: 152262 Hom.: 0 Cov.: 32 AF XY: 0.00109 AC XY: 81 AN XY: 74448

Gnomad4 AFR AF: 0.000626

Gnomad4 AMR AF: 0.000327

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000942

Gnomad4 NFE AF: 0.00193

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.00188 Hom.: 0

Bravo AF: 0.00111

TwinsUK AF: 0.00243 AC: 9

ALSPAC AF: 0.00285 AC: 11

ESP6500AA AF: 0.000454 AC: 2

ESP6500EA AF: 0.00314 AC: 27

ExAC AF: 0.00114 AC: 138

EpiCase AF: 0.00202

EpiControl AF: 0.00202

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:23

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Argininosuccinate lyase deficiency Pathogenic:16

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The ASL c.35G>A (p.Arg12Gln) missense variant is reported in two studies in at least nine individuals with argininosuccinate lyase deficiency, including eight compound heterozygotes and one individual in whom zygosity is not noted (Sampaleanu et al. 2001; Balmer et al. 2014). All reported individuals exhibited a mild phenotype. Control data are unavailable for this variant, which is reported at a frequency of 0.00314 in the European American population of the Exome Sequencing Project. Kinetic analysis of the p.Arg12Gln variant by Sampaleanu et al. (2001) showed the Kcat was reduced by 18-fold and the Km was decreased by 2-fold, and Hu et al. (2015) reported that the p.Arg12Gln variant had a specific activity of 4.3% of wild type when expressed in HEK293T cells. Based on the evidence, the p.Arg12Gln variant is classified as pathogenic for argininosuccinate lyase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Jul 28, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 15, 2023	Variant summary: ASL c.35G>A (p.Arg12Gln) results in a conservative amino acid change located in the fumarate lyase, N-terminal domain (IPR022761) of 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 0.0011 in 250818 control chromosomes in the gnomAD database, including 1 homozygote. This frequency is not significantly higher than estimated for a pathogenic variant in ASL causing Argininosuccinic Aciduria (0.0011 vs 0.0042), allowing no conclusion about variant significance. c.35G>A has been reported in the literature in multiple individuals affected with Argininosuccinic Aciduria, including at least one homozygote and one case where it was reported as a de novo occurrence (e.g. Mercimek-Mahmutoglu_2010, Balmer_2014, Al-Hashim_2016). These data indicate that the variant is very likely to be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function and both found that the variant effect results in equal to or less than 10% of normal activity (e.g. Sampaleanu_2001, Hu_2015). Sixteen submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic (n=10)/likely pathogenic (n=6). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jul 02, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 31, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	DASA	Jan 05, 2022	The c.35G>A;p.(Arg12Gln) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID 92360; 20236848; 24166829; 28251416) - PS4. Well-established in vitro or in vivo functional studies support a damaging effect on the gene or gene product (PMID: 25778938) - PS3_supporting. The variant is present at low allele frequencies population databases (rs145138923– gnomAD 0.01163%; ABraOM 0.001281 frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Arg12Gln) was detected in trans with a pathogenic variant (PMID: 20236848: 26661037; 28251416) - PM3_very strong The variant was assumed de novo, but without confirmation of paternity and maternity (PMID: 26661037) - PM6. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Dec 29, 2015	The p.Arg12Gln variant in ASL, after its first description by Sampaleanu et al. 2001, has been reported in at least 11 individuals with Argininosuccinate lyase deficiency (Balmer 2014, Mercimek-Mahmutoglu 2010) both in the homozygous and the compound heterozygous state. This variant has been identified in 0.18% (118/65326) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs145138923). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In addition, computational prediction tools and conservation analysis suggest that the p.Arg12Gln variant may impact the protein. In summary, this variant meets our criteria to be classified as pathogenic for Arginosuccinate lyase deficiency in an autosomal recessive manner. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Nov 04, 2021	NM_001024943.1(ASL):c.35G>A(R12Q) is a missense variant classified as likely pathogenic in the context of argininosuccinic aciduria. Please note that R12Q is associated with a broad spectrum of disease, ranging from clinically asymptomatic to classic argininosuccinic aciduria. R12Q has been observed in cases with relevant disease (PMID: 28251416, 24166829, 31943503, 31056765). Functional assessments of this variant are available in the literature (PMID: 11747432, 25778938, 31943503). R12Q has been observed in population frequency databases (gnomAD: NFE 0.19%). In summary, NM_001024943.1(ASL):c.35G>A(R12Q) is a missense variant that has functional 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	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Feb 16, 2023	PM3_Very strong, PS3, PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 12 of the ASL protein (p.Arg12Gln). This variant is present in population databases (rs145138923, gnomAD 0.2%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with argininosuccinic aciduria (PMID: 20236848, 24166829, 26661037). ClinVar contains an entry for this variant (Variation ID: 92360). 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 ASL protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects ASL function (PMID: 11747432, 25778938). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	Mar 18, 2022	ACMG classification criteria: PS3 supporting, PM3 very strong, PP3 supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Mar 07, 2015	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	New York Genome Center	Aug 20, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 27, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Aug 10, 2021	This sequence change is predicted to replace arginine with glutamine at codon 12 of the ASL protein (p.(Arg12Gln)). The arginine residue is evolutionarily conserved (100 vertebrates, UCSC), and is located in the lyase 1 domain. There is a small physicochemical difference between arginine and glutamine. The variant is present in a large population cohort at a frequency of 0.1% (rs145138923, 316/282,204 alleles, 1 homozygote in gnomAD v2.1). The variant has been identified in a homozygous state and compound heterozygous with a second allele in multiple individuals with a phenotype ranging from asymptomatic to agenesis of the corpus callosum or moderate intellectual disability with mild cerebellar atrophy (PMID: 20236848, 24166829, 26661037, 28251416). Impaired enzyme activity has been measured in patient red blood cells and in vitro functional assays expressing the variant (PMID: 11747432, 20236848, 25778938). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (6/6 algorithms). Based on the classification scheme RMH ACMG Guidelines v1.4.0, this variant is classified as LIKELY PATHOGENIC. Following criteria are met: PM3_Strong, PS3_Supporting, PP3, PP4. -

not provided Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 28, 2023	Functional expression studies demonstrate reduced activity of the R12Q variant compared to the wild type protein (Hu et al., 2015); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 12384776, 31589614, 11747432, 29773863, 26661037, 25087612, 23757202, 31943503, 20236848, 34405919, 24166829, 25778938, 31980526, 28251416) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Oct 31, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 21, 2013	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 24, 2021

The c.35G>A (p.R12Q) alteration is located in exon 3 (coding exon 2) of the ASL gene. This alteration results from a G to A substitution at nucleotide position 35, causing the arginine (R) at amino acid position 12 to be replaced by a glutamine (Q). Based on data from gnomAD, the A allele has an overall frequency of 0.11% (316/282204) total alleles studied. The highest observed frequency was 0.19% (244/128664) of European (non-Finnish) alleles. This variant has been reported in the homozygous and compound heterozygous states in several individuals with clinical and/or biochemical features of argininosuccinic acid lyase deficiency (ASLD), although several individuals with reduced enzyme activity were clinically asymptomatic or only mildly affected, which suggests that this variant may be a hypomorphic variant with incomplete penetrance (Mercimek-Mahmutoglu, 2010; Balmer, 2014; Baruteau, 2017). In addition, a recent case-control analysis shows that this alteration is significantly enriched in an ASLD cohort compared to matched controls (Mikó, 2021). This amino acid position is highly conserved in available vertebrate species. In vitro functional studies demonstrate that this alteration leads to reduced enzyme activity when expressed in conjunction with a null allele or in homozygosity (Hu, 2015; Zielonka, 2020). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

ASL-related condition Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 19, 2024

The ASL c.35G>A variant is predicted to result in the amino acid substitution p.Arg12Gln. This variant has been reported in the homozygous and compound heterozygous state in individuals with argininosuccinate lyase deficiency (Balmer et al. 2014. PubMed ID: 24166829). In the homozygous state, the p.Arg12Gln substitution was associated with an attenuated course of disease (Balmer et al. 2014. PubMed ID: 24166829). In functional studies, the activity of the argininosuccinate lyase enzyme containing the p.Arg12Gln substitution was decreased relative to wild-type (Sampaleanu et al. 2001. PubMed ID: 11747432; Hu et al. 2015. PubMed ID: 25778938). This variant is reported in 0.19% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.67
BayesDel_addAF	Pathogenic	0.26	D
BayesDel_noAF	Pathogenic	0.60
Cadd	Pathogenic	33
Dann	Pathogenic	1.0
DEOGEN2	Pathogenic	0.93	D;.;D;.
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.93
FATHMM_MKL	Pathogenic	1.0	D
M_CAP	Pathogenic	0.98	D
MetaRNN	Uncertain	0.72	D;D;D;D
MetaSVM	Pathogenic	0.99	D
MutationAssessor	Pathogenic	4.1	H;H;H;H
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.72	T
PROVEAN	Uncertain	-3.6	D;D;D;D
REVEL	Pathogenic	0.98
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D
Polyphen		1.0	D;.;D;.
Vest4		0.87
MVP		0.99
MPC		1.0
ClinPred		0.89	D
GERP RS		4.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.97
gMVP		0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs145138923; hg19: chr7-65546812; COSMIC: COSV59188498;