VCV002581413.2 - ClinVar

NM_000048.4(ASL):c.434A>G (p.Asp145Gly)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000048.4(ASL):c.434A>G (p.Asp145Gly)

Variation ID: 2581413 Accession: VCV002581413.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 7q11.21 7: 66083162 (GRCh38) [ NCBI UCSC ] 7: 65548149 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 7, 2023	Dec 30, 2023	Aug 29, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_000048.4:c.434A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000039.2:p.Asp145Gly	missense
NM_001024943.2:c.434A>G	NP_001020114.1:p.Asp145Gly	missense
NM_001024944.2:c.434A>G	NP_001020115.1:p.Asp145Gly	missense
NM_001024946.2:c.434A>G	NP_001020117.1:p.Asp145Gly	missense
NC_000007.14:g.66083162A>G
NC_000007.13:g.65548149A>G
NG_009288.1:g.12374A>G

... more HGVS ... less HGVS

Protein change

D145G

Other names

Canonical SPDI

NC_000007.14:66083161:A:G

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
ASL		-	-	GRCh38 GRCh37	858	894

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Uncertain significance (1)	criteria provided, single submitter	Aug 29, 2023	RCV003331818.1
Argininosuccinate lyase deficiency	Likely pathogenic (1)	criteria provided, single submitter	Mar 23, 2023	RCV003475563.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Aug 29, 2023)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV004037661.1 First in ClinVar: Oct 07, 2023 Last updated: Oct 07, 2023	Publications: PubMed (3) PubMed: 31183366‚ 26843370‚ 24927999 Comment: Variant summary: ASL c.434A>G (p.Asp145Gly) results in a non-conservative amino acid change located in the Fumarate lyase, N-terminal domain (IPR022761) of the encoded protein sequence. … (more) Variant summary: ASL c.434A>G (p.Asp145Gly) results in a non-conservative amino acid change located in the Fumarate lyase, N-terminal domain (IPR022761) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Three predict the variant creates a cryptic 5 donor site. In addition, Wen_2016 showed this variant led to the skipping of exon 5. The variant was absent in 249972 control chromosomes (gnomAD). c.434A>G has been reported in the literature in individuals affected with Argininosuccinic Aciduria (Wen_2014, Wen_2016). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 31183366, 26843370, 24927999). No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. (less)
Likely pathogenic (Mar 23, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Argininosuccinate lyase deficiency Affected status: unknown Allele origin: unknown	Baylor Genetics Accession: SCV004201251.1 First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023

Comment:

Variant summary: ASL c.434A>G (p.Asp145Gly) results in a non-conservative amino acid change located in the Fumarate lyase, N-terminal domain (IPR022761) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Three predict the variant creates a cryptic 5 donor site. In addition, Wen_2016 showed this variant led to the skipping of exon 5. The variant was absent in 249972 control chromosomes (gnomAD). c.434A>G has been reported in the literature in individuals affected with Argininosuccinic Aciduria (Wen_2014, Wen_2016). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 31183366, 26843370, 24927999). No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Whole-Exome Sequencing Identified a Novel Compound Heterozygous Genotype in ASL in a Chinese Han Patient with Argininosuccinate Lyase Deficiency.	Zhao M	BioMed research international	2019	PMID: 31183366
NGS in argininosuccinic aciduria detects a mutation (D145G) which drives alternative splicing of ASL: a case report study.	Wen W	BMC medical genetics	2016	PMID: 26843370
[Genetic analysis of ASS1, ASL and SLC25A13 in citrullinemia patients].	Wen P	Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics	2014	PMID: 24927999

Text-mined citations for this variant ...

Record last updated Dec 30, 2023

ClinVar Genomic variation as it relates to human health

NM_000048.4(ASL):c.434A>G (p.Asp145Gly)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...