VCV002050208.4 - ClinVar

NM_025233.7(COASY):c.1388-2A>G

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.

(3)

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.

Likely pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_025233.7(COASY):c.1388-2A>G

Variation ID: 2050208 Accession: VCV002050208.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 17q21.2 17: 42565469 (GRCh38) [ NCBI UCSC ] 17: 40717487 (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	Feb 8, 2023	Nov 24, 2024	Feb 5, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_025233.7:c.1388-2A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice acceptor
NM_001042529.3:c.1388-2A>G		splice acceptor
NM_001042532.4:c.1475-2A>G		splice acceptor
NM_025233.6:c.1388-2A>G
NC_000017.11:g.42565469A>G
NC_000017.10:g.40717487A>G
NG_029442.1:g.3410A>G
NG_034110.1:g.8396A>G
NG_136593.1:g.218A>G

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000017.11:42565468: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.
COASY		-	-	GRCh38 GRCh37	306	328

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.
Neurodegeneration with brain iron accumulation 6	Likely pathogenic (1)	criteria provided, single submitter	Jan 20, 2024	RCV002937500.3
COASY-related disorder	Likely pathogenic (1)	criteria provided, single submitter	Jan 11, 2023	RCV003395537.4
not provided	Likely pathogenic (1)	criteria provided, single submitter	Feb 5, 2024	RCV004790277.1

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.
Likely pathogenic (Jan 11, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	COASY-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004120501.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023	Comment: The COASY c.1388-2A>G variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant was reported in a carrier … (more) The COASY c.1388-2A>G variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant was reported in a carrier study for rare recessive Mendelian diseases in a Brazilian cohort (Quaio et al 2021. PubMed ID: 34269512). This variant is reported in 0.17% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-40717487-A-G). Variants that disrupt the consensus splice acceptor site in COASY are expected to be pathogenic. This variant is interpreted as likely pathogenic. (less)
Likely pathogenic (Jan 20, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Neurodegeneration with brain iron accumulation 6 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003259446.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 14, 2024	Publications: PubMed (3) PubMed: 16199547‚ 24360804‚ 30089828 Comment: This sequence change affects an acceptor splice site in intron 6 of the COASY gene. It is expected to disrupt RNA splicing. Variants that disrupt … (more) This sequence change affects an acceptor splice site in intron 6 of the COASY gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in COASY are known to be pathogenic (PMID: 24360804, 30089828). This variant is present in population databases (rs145108650, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with COASY-related conditions. ClinVar contains an entry for this variant (Variation ID: 2050208). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. (less)
Likely pathogenic (Feb 05, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Not provided Affected status: unknown Allele origin: germline	Mayo Clinic Laboratories, Mayo Clinic Accession: SCV005413220.1 First in ClinVar: Nov 24, 2024 Last updated: Nov 24, 2024	Publications: PubMed (2) PubMed: 34269512‚ 36939041 Comment: PM2, PVS1 Number of individuals with the variant: 1

Comment:

The COASY c.1388-2A>G variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant was reported in a carrier study for rare recessive Mendelian diseases in a Brazilian cohort (Quaio et al 2021. PubMed ID: 34269512). This variant is reported in 0.17% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-40717487-A-G). Variants that disrupt the consensus splice acceptor site in COASY are expected to be pathogenic. This variant is interpreted as likely pathogenic.

Comment:

This sequence change affects an acceptor splice site in intron 6 of the COASY gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in COASY are known to be pathogenic (PMID: 24360804, 30089828). This variant is present in population databases (rs145108650, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with COASY-related conditions. ClinVar contains an entry for this variant (Variation ID: 2050208). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely 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
Evaluation of an automated genome interpretation model for rare disease routinely used in a clinical genetic laboratory.	Meng L	Genetics in medicine : official journal of the American College of Medical Genetics	2023	PMID: 36939041
Frequency of carriers for rare recessive Mendelian diseases in a Brazilian cohort of 320 patients.	Quaio CRDC	American journal of medical genetics. Part C, Seminars in medical genetics	2021	PMID: 34269512
Biallelic loss of function variants in COASY cause prenatal onset pontocerebellar hypoplasia, microcephaly, and arthrogryposis.	van Dijk T	European journal of human genetics : EJHG	2018	PMID: 30089828
Exome sequence reveals mutations in CoA synthase as a cause of neurodegeneration with brain iron accumulation.	Dusi S	American journal of human genetics	2014	PMID: 24360804
Splicing in action: assessing disease causing sequence changes.	Baralle D	Journal of medical genetics	2005	PMID: 16199547

Text-mined citations for this variant ...

Record last updated Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_025233.7(COASY):c.1388-2A>G

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...