ClinVar Genomic variation as it relates to human health
NM_001243279.3(ACSF3):c.1075G>A (p.Glu359Lys)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001243279.3(ACSF3):c.1075G>A (p.Glu359Lys)
Variation ID: 31136 Accession: VCV000031136.36
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 16q24.3 16: 89114436 (GRCh38) [ NCBI UCSC ] 16: 89180844 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Apr 27, 2016 Oct 20, 2024 Mar 30, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001243279.3:c.1075G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001230208.1:p.Glu359Lys missense NM_001127214.4:c.1075G>A NP_001120686.1:p.Glu359Lys missense NM_001284316.2:c.280G>A NP_001271245.1:p.Glu94Lys missense NM_174917.5:c.1075G>A NP_777577.2:p.Glu359Lys missense NR_104293.2:n.1413G>A non-coding transcript variant NR_147928.2:n.1413G>A non-coding transcript variant NC_000016.10:g.89114436G>A NC_000016.9:g.89180844G>A NG_031961.1:g.25628G>A Q4G176:p.Glu359Lys - Protein change
- E359K, E94K
- Other names
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p.E359K:GAG>AAG
- Canonical SPDI
- NC_000016.10:89114435:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe 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.
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0.00080 (A)
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Allele frequency
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The frequency of the allele represented by this VCV record.
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1000 Genomes Project 30x 0.00062
The Genome Aggregation Database (gnomAD), exomes 0.00067
Exome Aggregation Consortium (ExAC) 0.00069
The Genome Aggregation Database (gnomAD) 0.00071
Trans-Omics for Precision Medicine (TOPMed) 0.00078
1000 Genomes Project 0.00080
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00085
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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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. |
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ACSF3 | - | - |
GRCh38 GRCh37 |
881 | 1082 | |
LOC125177393 | - | - | - | GRCh38 | - | 120 |
Conditions - Germline
Condition
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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. |
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Pathogenic/Likely pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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Mar 30, 2024 | RCV000024132.21 | |
Pathogenic/Likely pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Feb 1, 2024 | RCV000185748.24 | |
Pathogenic (1) |
no assertion criteria provided
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Sep 16, 2020 | RCV001274019.1 | |
ACSF3-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Nov 21, 2023 | RCV003415738.6 |
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. |
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Pathogenic
(Sep 19, 2022)
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criteria provided, single submitter
Method: clinical testing
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Combined malonic and methylmalonic acidemia
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001467827.2
First in ClinVar: Jan 09, 2021 Last updated: Nov 05, 2022 |
Comment:
Variant summary: ACSF3 c.1075G>A (p.Glu359Lys) results in a conservative amino acid change located in the AMP-dependent synthetase/ligase domain (IPR000873) of the encoded protein sequence. Four … (more)
Variant summary: ACSF3 c.1075G>A (p.Glu359Lys) results in a conservative amino acid change located in the AMP-dependent synthetase/ligase domain (IPR000873) 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 0.00067 in 250734 control chromosomes (gnomAD). c.1075G>A has been reported in the literature as a biallelic genotype in multiple individuals affected with Combined Malonic And Methylmalonic Aciduria (CMAMMA) presenting with elevated levels of MA and/or MMA in urine and/or plasma samples (e.g. Alfares_2011, Sloan_2011, Brasil_2018, Levtova_2019). These data indicate that the variant is very likely to be associated with disease. Several publications report experimental evidence evaluating the effects of the variant in-vitro. One study showed that cells derived from patients harboring the variant have increased accumulation of MMA in the media, and the expression of wild-type ACSF3 in these cells restores the media MMA to levels similar to controls (e.g. Sloan_2011). Another study demonstrated that cells from a homozygous patient have altered metabolic profiles as determined by Seahorse assays (e.g. Wehbe_2019). Six submitters have provided clinical-significance assessments for this variant to ClinVar after 2014. The majority of submitters classified the variant as either pathogenic (n=3) or likely pathogenic (n=1), and two submitters classified it as VUS. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Likely pathogenic
(Mar 30, 2024)
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criteria provided, single submitter
Method: clinical testing
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Combined malonic and methylmalonic acidemia
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV001522238.3
First in ClinVar: Mar 22, 2021 Last updated: Jun 17, 2024 |
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Pathogenic
(Nov 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000238677.16
First in ClinVar: Jul 18, 2015 Last updated: Nov 25, 2023 |
Comment:
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: 21785126, … (more)
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: 21785126, 29858964, 21841779, 26915364, 34426522, 32944792, 31980526, 34440436, 33879512) (less)
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Pathogenic
(May 23, 2022)
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criteria provided, single submitter
Method: clinical testing
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Combined malonic and methylmalonic acidemia
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV004175671.1
First in ClinVar: Dec 17, 2023 Last updated: Dec 17, 2023 |
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Likely pathogenic
(Jun 08, 2022)
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criteria provided, single submitter
Method: clinical testing
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Combined malonic and methylmalonic acidemia
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002021285.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
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Combined malonic and methylmalonic acidemia
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000771501.5
First in ClinVar: Apr 27, 2016 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 359 of the ACSF3 protein … (more)
This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 359 of the ACSF3 protein (p.Glu359Lys). This variant is present in population databases (rs150487794, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with combined malonic and methylmalonic aciduria (PMID: 21785126, 21841779, 26915364, 30740739; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 31136). 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 ACSF3 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. (less)
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Likely pathogenic
(Feb 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not provided
Affected status: unknown
Allele origin:
germline
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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV004226685.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
PP1, PP3, PM3_strong
Number of individuals with the variant: 1
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Pathogenic
(Feb 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV004701707.8
First in ClinVar: Mar 10, 2024 Last updated: Oct 20, 2024 |
Comment:
ACSF3: PM3:Very Strong, PM2:Supporting, PP3
Number of individuals with the variant: 1
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Pathogenic
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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Methylmalonic acidemia
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001457701.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Pathogenic
(Aug 14, 2011)
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no assertion criteria provided
Method: literature only
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COMBINED MALONIC AND METHYLMALONIC ACIDURIA
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000045423.4
First in ClinVar: Apr 04, 2013 Last updated: Jul 29, 2023 |
Comment on evidence:
In a woman with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified compound heterozygosity for a G-to-A transition at nucleotide 1075 … (more)
In a woman with combined malonic and methylmalonic aciduria (CMAMMA; 614265), Sloan et al. (2011) identified compound heterozygosity for a G-to-A transition at nucleotide 1075 in exon 6 of the ACSF3 gene, resulting in a glu-to-lys substitution at codon 359 (E359K). The patient presented at age 55 with psychiatric symptoms and T2 hyperintensities on brain MRI and died at the age of 60. The other allele of the patient carried the R558W mutation (614245.0001). The E359K mutation occurs in motif III, involved in substrate binding, of the ACSF3 gene. In a 4-year-old French Canadian girl (patient 2) with CMAMMA detected through the Quebec newborn urine screening program, Alfares et al. (2011) identified a homozygous c.1075G-A transition in the ACSF3 gene, resulting in a glu359-to-lys (E359K) substitution. The mutation, which was identified by whole-exome sequencing, was said to occur in exon 5. The patient was born at term and was clinically asymptomatic; she had normal cardiac examinations and age-appropriate development. She had a similarly affected 2-year-old brother who was also homozygous for the mutation. The parents were heterozygous for the mutation. (less)
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Pathogenic
(Nov 21, 2023)
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no assertion criteria provided
Method: clinical testing
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ACSF3-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004109332.3
First in ClinVar: Nov 20, 2023 Last updated: Oct 08, 2024 |
Comment:
The ACSF3 c.1075G>A variant is predicted to result in the amino acid substitution p.Glu359Lys. This variant has been reported in both the compound heterozygous and … (more)
The ACSF3 c.1075G>A variant is predicted to result in the amino acid substitution p.Glu359Lys. This variant has been reported in both the compound heterozygous and homozygous states in multiple unrelated individuals diagnosed with combined malonic and methylmalonic aciduria (CMAMMA) (Alfares et al. 2011. PubMed ID: 21785126; Sloan et al. 2011. PubMed ID: 21841779; de Sain-van der Velden et al. 2016. PubMed ID: 26915364; Brasil et al. 2018. PubMed ID: 30041674). It has been found to be one of the most commonly reported causative variants in ACSF3 (Levtova et al. 2019. PubMed ID: 30740739). This variant is reported in 0.11% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. (less)
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Uncertain significance
(Jun 10, 2015)
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Flagged submission
flagged submission
Method: clinical testing
Reason: Outlier claim with insufficient supporting evidence
Source: ClinGen
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000331886.4
First in ClinVar: Dec 06, 2016 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 3
Sex: mixed
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Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more |
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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Personalised virtual gene panels reduce interpretation workload and maintain diagnostic rates of proband-only clinical exome sequencing for rare disorders. | Molina-Ramírez LP | Journal of medical genetics | 2022 | PMID: 33879512 |
Combined Malonic and Methylmalonic Aciduria Due to ACSF3 Variants Results in Benign Clinical Course in Three Chinese Patients. | Wang P | Frontiers in pediatrics | 2021 | PMID: 34900860 |
Utility of Gene Panels for the Diagnosis of Inborn Errors of Metabolism in a Metabolic Reference Center. | Barbosa-Gouveia S | Genes | 2021 | PMID: 34440436 |
The genetic structure of the Turkish population reveals high levels of variation and admixture. | Kars ME | Proceedings of the National Academy of Sciences of the United States of America | 2021 | PMID: 34426522 |
Pediatric recurrent Rosai-Dorfman disease with germline heterozygous SLC29A3 and somatic MAP2K1 mutations. | Suryaprakash S | Annals of hematology | 2020 | PMID: 32944792 |
Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging. | Hou YC | Proceedings of the National Academy of Sciences of the United States of America | 2020 | PMID: 31980526 |
The emerging role of the mitochondrial fatty-acid synthase (mtFASII) in the regulation of energy metabolism. | Wehbe Z | Biochimica et biophysica acta. Molecular and cell biology of lipids | 2019 | PMID: 31376476 |
Combined malonic and methylmalonic aciduria due to ACSF3 mutations: Benign clinical course in an unselected cohort. | Levtova A | Journal of inherited metabolic disease | 2019 | PMID: 30740739 |
Improving the diagnosis of cobalamin and related defects by genomic analysis, plus functional and structural assessment of novel variants. | Brasil S | Orphanet journal of rare diseases | 2018 | PMID: 30041674 |
A New Approach for Fast Metabolic Diagnostics in CMAMMA. | de Sain-van der Velden MG | JIMD reports | 2016 | PMID: 26915364 |
Next-generation sequencing to identify genetic causes of cardiomyopathies. | Norton N | Current opinion in cardiology | 2012 | PMID: 22421630 |
Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria. | Sloan JL | Nature genetics | 2011 | PMID: 21841779 |
Combined malonic and methylmalonic aciduria: exome sequencing reveals mutations in the ACSF3 gene in patients with a non-classic phenotype. | Alfares A | Journal of medical genetics | 2011 | PMID: 21785126 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ACSF3 | - | - | - | - |
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Text-mined citations for rs150487794 ...
HelpRecord last updated Oct 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.