NM_054012.4(ASS1):c.1168G>A (p.Gly390Arg) AND Citrullinemia type I

Germline classification:: Pathogenic/Likely pathogenic (15 submissions)
Last evaluated:: Mar 28, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000006701.40

Allele description [Variation Report for NM_054012.4(ASS1):c.1168G>A (p.Gly390Arg)]

NM_054012.4(ASS1):c.1168G>A (p.Gly390Arg)

Gene:

ASS1:argininosuccinate synthase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_054012.4(ASS1):c.1168G>A (p.Gly390Arg)

Other names:

p.G390R:GGG>AGG

HGVS:

NC_000009.12:g.130499545G>A
NG_011542.1:g.59839G>A
NM_000050.4:c.1168G>A
NM_054012.4:c.1168G>AMANE SELECT
NP_000041.2:p.Gly390Arg
NP_000041.2:p.Gly390Arg
NP_446464.1:p.Gly390Arg
NC_000009.11:g.133374932G>A
NM_054012.3:c.1168G>A
NM_054012.4:c.1168G>A
P00966:p.Gly390Arg

Protein change:

G390R; GLY390ARG

Links:

UniProtKB: P00966#VAR_000694; OMIM: 603470.0009; dbSNP: rs121908641

NCBI 1000 Genomes Browser:

rs121908641

Molecular consequence:

NM_000050.4:c.1168G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_054012.4:c.1168G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Citrullinemia type I (CTNL1)
Synonyms:: ASS DEFICIENCY; Classic citrullinemia; Citrullinemia 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008988; MedGen: C4721769; Orphanet: 247525; OMIM: 215700

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000026892	OMIM	no assertion criteria provided	Pathogenic (Mar 1, 2009)	germline	literature only	PubMed (1) [See all records that cite this PMID] Kobayashi, K., Jackson, M. J., Tick, D. B., O'Brien, W. E., Beaudet, A. L. Characterization of nine mutant alleles causing citrullinemia. (Abstract) Am. J. Hum. Genet. 45 (suppl.): A201-only, 1989.,
SCV000323098	GeneReviews	no classification provided	not provided	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 12815590, 11941481
SCV000611160	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 18, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000694161	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Apr 12, 2016)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25433810, 18473344 LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV000787654	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	no assertion criteria provided	Likely pathogenic (Aug 29, 2016)	germline	clinical testing
SCV001163604	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 27, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001193921	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019))	Likely pathogenic (Nov 12, 2019)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 18473344, 16475226, 12815590, 7557970 Citation Link,
SCV001368809	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 31, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001453094	Natera, Inc.	no assertion criteria provided	Pathogenic (Sep 16, 2020)	germline	clinical testing
SCV001810277	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 22, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002019943	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 9, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002053825	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	inherited	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004047075	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004847114	Genomic Medicine Lab, University of California San Francisco	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 4, 2023)	biparental	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004848784	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 28, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	biparental	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	inherited	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
Hindu/Gujarati	germline	no	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations and polymorphisms in the human argininosuccinate synthetase (ASS1) gene.

Engel K, Höhne W, Häberle J.

Hum Mutat. 2009 Mar;30(3):300-7. doi: 10.1002/humu.20847. Review.

PubMed [citation]

PMID:: 19006241

Structure of the human argininosuccinate synthetase gene and an improved system for molecular diagnostics in patients with classical and mild citrullinemia.

Häberle J, Pauli S, Linnebank M, Kleijer WJ, Bakker HD, Wanders RJ, Harms E, Koch HG.

Hum Genet. 2002 Apr;110(4):327-33. Epub 2002 Mar 1.

PubMed [citation]

PMID:: 11941481

See all PubMed Citations (8)

Details of each submission

From OMIM, SCV000026892.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

Kobayashi et al. (1989) demonstrated a change in codon 390 in the ASS gene, GGC (gly) to AGG (arg), in a case of citrullinemia (215700). Five of the 6 single base mutations involved C:G to T:A transitions in CpG dinucleotides.

In a review, Engel et al. (2009) stated that the G390R mutation is the most common mutation in patients with the classic phenotype of citrullinemia.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneReviews, SCV000323098.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV000611160.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694161.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: The ASS1 c.1168G>A variant affects a conserved nucleotide, resulting in amino acid change from Gly to Arg. Gly390 is located in a-helix 12 and is important for intermolecular contact of the multimerization tails, and 5/5 in-silico tools predict damaging outcome for this variant. The enzymatic ASS activity of G390R was shown to be below 2% of the wild-type protein (Berning_HM_2008). This variant was found in 45/113324 control chromosomes at a frequency of 0.0003971, which does not exceed maximal expected frequency of a pathogenic ASS1 allele (0.0040825). This variant is reported as the most common mutation in patients with the classic phenotype of citrullinemia. In addition, several clinical laboratories classified this variant as pathogenic. Taken together, this variant was classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV000787654.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Hindu/Gujarati	1	not provided	not provided	clinical testing	not provided
2	Hindu/Gujarati	1	not provided	not provided	clinical testing	not provided

Description

The observed variant c.1168G>A (p.Gly390Arg) is not reported in 1000 Genomes and has a minor allele frequency of 0.00040 in ExAC databases. The in silico prediction of the variant is disease causing by MutationTaster2, damaging by SIFT and probably damaging by Polyphen2.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		1	not provided	not provided	not provided
2	germline	no	not provided	not provided	not provided		1	not provided	not provided	not provided

From Baylor Genetics, SCV001163604.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Myriad Genetics, Inc., SCV001193921.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

NM_000050.4(ASS1):c.1168G>A(G390R) is classified as likely pathogenic in the context of citrullinemia type 1. Sources cited for classification include the following: PMID 18473344, 16475226, 12815590, and 7557970. Classification of NM_000050.4(ASS1):c.1168G>A(G390R) is based on the following criteria: There is strong evidence of association with the variant and the relevant disease and there is functional data showing deficient protein function. Please note: this variant was assessed in the context of healthy population screening.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001368809.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM2,PM3,PP3,PP4.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV001453094.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV001810277.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002019943.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV002053825.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047075.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The c.1168G>A (p.Gly390Arg) missense variant in ASS1 gene has been reported in homozygous state in individuals affected with citrullinemia (Laróvere et al., 2012). Experimental studies have shown that this variant disrupts the function and substantially reduces the activity of the encoded enzyme in vitro (Berning et al., 2008). This variant is reported with the allele frequency (0.03%) in the gnomad and novel in 1000 genome database. This variant has been reported to the ClinVar database as Pathogenic/Likely Pathogenic. The amino acid Gly at position 390 is changed to a Arg changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genomic Medicine Lab, University of California San Francisco, SCV004847114.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	biparental	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV004848784.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The p.Gly390Arg variant in AAS1 has been reported in >30 individuals with citrullinemia type I (both in the homozygous and compound heterozygous state) and segregated with disease in at least 5 affected relatives from 5 families. It is the most common variant identified in patients with the classical phenotype (Vilaseca 2001 PMID: 11708871, Gao 2003 PMID: 12815590, Berning 2008 PMID: 18473344, Engel 2009 PMID: 19006241, Laróvere 2009 PMID: 19358837, Laróvere 2012 PMID: 23430935). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID: 6329) and has been identified in 0.06% (3/4828) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). In vitro functional studies provide some evidence that this variant impacts protein function, demonstrating less than 2% of wild type argininosuccinate synthetase activity (Berning 2008 PMID: 18473344, Shaheen 1994PMID: 8792870) and computational prediction tools and conservation analyses are consistent with pathogenicity. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive citrullinemia type I. ACMG/AMP Criteria applied: PM3_Very Strong, PP1_Moderate, PS3_Supporting, PP3.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jan 13, 2025

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