VCV002675982.3 - ClinVar

NM_000183.3(HADHB):c.1389+5G>A

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.

Pathogenic/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_000183.3(HADHB):c.1389+5G>A

Variation ID: 2675982 Accession: VCV002675982.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 2p23.3 2: 26285576 (GRCh38) [ NCBI UCSC ] 2: 26508444 (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	Dec 30, 2023	Jun 17, 2024	Feb 7, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_000183.3:c.1389+5G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_001281512.2:c.1344+5G>A		intron variant
NM_001281513.2:c.1323+5G>A		intron variant
NC_000002.12:g.26285576G>A
NC_000002.11:g.26508444G>A
NG_007294.1:g.45624G>A

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000002.12:26285575:G:A

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.
HADHB		-	-	GRCh38 GRCh37	554	585

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.
Mitochondrial trifunctional protein deficiency	Pathogenic (1)	criteria provided, single submitter	Feb 27, 2023	RCV003468324.4
Mitochondrial trifunctional protein deficiency 1	Likely pathogenic (1)	criteria provided, single submitter	Feb 7, 2024	RCV004574035.1

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 (Feb 07, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Mitochondrial trifunctional protein deficiency 1 Affected status: unknown Allele origin: unknown	Baylor Genetics Accession: SCV004191814.2 First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024
Pathogenic (Feb 27, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Mitochondrial trifunctional protein deficiency Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004651364.1 First in ClinVar: Feb 28, 2024 Last updated: Feb 28, 2024	Publications: PubMed (3) PubMed: 34543737‚ 17576681‚ 9536098 Comment: This sequence change falls in intron 15 of the HADHB gene. It does not directly change the encoded amino acid sequence of the HADHB protein. … (more) This sequence change falls in intron 15 of the HADHB gene. It does not directly change the encoded amino acid sequence of the HADHB protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has been observed in individual(s) with clinical features of HADHB-related conditions (PMID: 34543737). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 15, but is expected to preserve the integrity of the reading-frame (PMID: 34543737). For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

This sequence change falls in intron 15 of the HADHB gene. It does not directly change the encoded amino acid sequence of the HADHB protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has been observed in individual(s) with clinical features of HADHB-related conditions (PMID: 34543737). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 15, but is expected to preserve the integrity of the reading-frame (PMID: 34543737). For these reasons, this variant has been classified as 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
Hypoparathyroidism, neutropenia and nephrotic syndrome in a patient with mitochondrial trifunctional protein deficiency: A case report and review of the literature.	Li Y	European journal of medical genetics	2021	PMID: 34543737
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.	Buratti E	Nucleic acids research	2007	PMID: 17576681
Statistical features of human exons and their flanking regions.	Zhang MQ	Human molecular genetics	1998	PMID: 9536098

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_000183.3(HADHB):c.1389+5G>A

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...