NM_054012.4(ASS1):c.689G>C (p.Gly230Ala) AND Citrullinemia type I

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Mar 14, 2023
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:: RCV000490502.4

Allele description [Variation Report for NM_054012.4(ASS1):c.689G>C (p.Gly230Ala)]

NM_054012.4(ASS1):c.689G>C (p.Gly230Ala)

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.689G>C (p.Gly230Ala)

HGVS:

NC_000009.12:g.130479716G>C
NG_011542.1:g.40010G>C
NG_053681.1:g.1557G>C
NM_000050.4:c.689G>C
NM_054012.4:c.689G>CMANE SELECT
NP_000041.2:p.Gly230Ala
NP_446464.1:p.Gly230Ala
NC_000009.11:g.133355103G>C

Protein change:

G230A

Links:

dbSNP: rs1085307056

NCBI 1000 Genomes Browser:

rs1085307056

Molecular consequence:

NM_000050.4:c.689G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_054012.4:c.689G>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Citrullinemia type I (CTNL1)
Synonyms:: Classic citrullinemia; ASS deficiency; 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
SCV000267214	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 18, 2016)	germline	reference population	PubMed (2) [See all records that cite these PMIDs] 23099195, 25741868
SCV002012030	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 2, 2021)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23099195, 25741868
SCV004205601	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 14, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000267214

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 18, 2016)

germline

reference population

PubMed (2)
[See all records that cite these PMIDs]

SCV002012030

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 2, 2021)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV004205601

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 14, 2023)

unknown

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	unknown	yes	1	not provided	not provided	1	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
East Asian	germline	unknown	1	not provided	not provided	not provided	not provided	reference population

Citations

PubMed

Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I.

Woo HI, Ki CS, Lee SY, Kim JW, Song J, Jin DK, Park WS, Lee DH, Lee YW, Park HD.

Clin Biochem. 2013 Feb;46(3):209-13. doi: 10.1016/j.clinbiochem.2012.10.008. Epub 2012 Oct 22.

PubMed [citation]

PMID:: 23099195

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267214.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East Asian	1	not provided	not provided	reference population	PubMed (2)

#	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		1	not provided	not provided	not provided

From 3billion, SCV002012030.1

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

Description

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic/likely pathogenic with supporting evidence (PMID: 23099195, PS1_P). It is not observed in the gnomAD v2.1.1 dataset (PM2). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.923, 3Cnet: 0.995, PP3). Patient is considered compatible with Snijders Citrullinemia (PP4_P).Therefore, this variant is classified as likley pathogenic according to the recommendation of ACMG/AMP guideline.

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

From Baylor Genetics, SCV004205601.1

#	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

Last Updated: Sep 29, 2024

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