VCV002427078.4 - ClinVar

NC_000006.11:g.(?_158532398)_(162868359_?)del

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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000006.11:g.(?_158532398)_(162868359_?)del

Variation ID: 2427078 Accession: VCV002427078.4

Type and length

Deletion, 4,335,962 bp

Location

Cytogenetic: 6q25.3-26 6: 158532398-162868359 (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 13, 2023	Nov 11, 2023	Jul 29, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NC_000006.11:g.(?_158532398)_(162868359_?)del

Protein change

Other names

Canonical SPDI

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.
IGF2R		No evidence available	No evidence available	GRCh38 GRCh37	160	189
ACAT2		-	-	GRCh38 GRCh37	28	61
AGPAT4		-	-	GRCh38 GRCh37	12	47
AIRN		-	-	GRCh38 GRCh37	-	23
DYNLT1		-	-	GRCh38 GRCh37	9	36
EZR		-	-	GRCh38 GRCh37	68	101
FNDC1		-	-	GRCh38 GRCh37	182	211
GTF2H5		-	-	GRCh38 GRCh37	61	91
LINC02901	-	-	-	GRCh38 GRCh37	-	26
LPA		-	-	GRCh38 GRCh37	152	187

There are 18 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37) and ClinGen Dosage Sensitivity Map.

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.
3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome	no classifications from unflagged records (1)	no classifications from unflagged records	-	RCV003122912.5
not provided	Pathogenic (1)	criteria provided, single submitter	Jul 29, 2022	RCV003122911.4

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.
Pathogenic (Jul 29, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003795410.2 First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023	Publications: PubMed (2) PubMed: 15220921‚ 26863999 Comment: A gross deletion of the genomic region encompassing the full coding sequence of the GTF2H5 gene has been identified. Loss-of-function variants in GTF2H5 are known … (more) A gross deletion of the genomic region encompassing the full coding sequence of the GTF2H5 gene has been identified. Loss-of-function variants in GTF2H5 are known to be pathogenic (PMID: 15220921, 26863999). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with GTF2H5-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)
Pathogenic (Jul 29, 2022)	Flagged submission flagged submission (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003795778 appears to (...more) Source: NCBI	3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003795778.2 First in ClinVar: Feb 13, 2023 Last updated: Nov 11, 2023	Publications: PubMed (1) PubMed: 22683713 Comment: A gross deletion of the genomic region encompassing the full coding sequence of the SERAC1 gene has been identified. Loss-of-function variants in SERAC1 are known … (more) A gross deletion of the genomic region encompassing the full coding sequence of the SERAC1 gene has been identified. Loss-of-function variants in SERAC1 are known to be pathogenic (PMID: 22683713). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with SERAC1-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)
Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more

Comment:

A gross deletion of the genomic region encompassing the full coding sequence of the GTF2H5 gene has been identified. Loss-of-function variants in GTF2H5 are known to be pathogenic (PMID: 15220921, 26863999). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with GTF2H5-related conditions. For these reasons, this variant has been classified as Pathogenic.

Comment:

A gross deletion of the genomic region encompassing the full coding sequence of the SERAC1 gene has been identified. Loss-of-function variants in SERAC1 are known to be pathogenic (PMID: 22683713). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with SERAC1-related conditions. 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
Whole Exome Sequencing in Pediatric Neurology Patients: Clinical Implications and Estimated Cost Analysis.	Nolan D	Journal of child neurology	2016	PMID: 26863999
Mutations in the phospholipid remodeling gene SERAC1 impair mitochondrial function and intracellular cholesterol trafficking and cause dystonia and deafness.	Wortmann SB	Nature genetics	2012	PMID: 22683713
A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A.	Giglia-Mari G	Nature genetics	2004	PMID: 15220921

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NC_000006.11:g.(?_158532398)_(162868359_?)del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...