VCV003063680.1 - ClinVar

NM_145199.3(LIPT1):c.368del (p.Lys123fs)

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.

(1)

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.

Uncertain significance

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_145199.3(LIPT1):c.368del (p.Lys123fs)

Variation ID: 3063680 Accession: VCV003063680.1

Type and length

Deletion, 1 bp

Location

Cytogenetic: 2q11.2 2: 99162318 (GRCh38) [ NCBI UCSC ] 2: 99778781 (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	Mar 30, 2024	Mar 30, 2024	Jan 25, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_145199.3:c.368del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_660200.1:p.Lys123fs	frameshift
NM_145199.3:c.368delA MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		frameshift
NM_001204830.2:c.368del	NP_001191759.1:p.Lys123fs	frameshift
NM_015929.4:c.368del	NP_057013.1:p.Lys123fs	frameshift
NM_145197.3:c.368del	NP_660198.1:p.Lys123fs	frameshift
NM_145198.3:c.368del	NP_660199.1:p.Lys123fs	frameshift
NR_037935.2:n.853del		non-coding transcript variant
NR_037936.2:n.517del		non-coding transcript variant
NC_000002.12:g.99162325del
NC_000002.11:g.99778788del
NG_050665.1:g.12371del

... more HGVS ... less HGVS

Protein change

K123fs

Other names

Canonical SPDI

NC_000002.12:99162317:AAAAAAAA:AAAAAAA

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.
LIPT1		-	-	GRCh38 GRCh37	14	134
MITD1	-	-	-	GRCh38 GRCh37	9	129

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	Jan 25, 2024	RCV003988268.1

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 (Jan 25, 2024)	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: SCV004803771.1 First in ClinVar: Mar 30, 2024 Last updated: Mar 30, 2024	Comment: Variant summary: LIPT1 c.368delA (p.Lys123SerfsX8) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein, … (more) Variant summary: LIPT1 c.368delA (p.Lys123SerfsX8) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein, however the molecular mechanism of disease attributed to LIPT1 is currently unknown. While this variant is not expected to result in nonsense mediated decay, it is predicted to disrupt the last 251 amino acids of the protein, including part of the Biotinyl protein ligase and lipoyl protein ligase, catalytic domain (IPR004143). The variant allele was found at a frequency of 6.4e-05 in 1609808 control chromosomes (gnomAD v4.0.0). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.368delA in individuals affected with Lipoyl Transferase 1 Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have reported clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. (less)

Comment:

Variant summary: LIPT1 c.368delA (p.Lys123SerfsX8) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein, however the molecular mechanism of disease attributed to LIPT1 is currently unknown. While this variant is not expected to result in nonsense mediated decay, it is predicted to disrupt the last 251 amino acids of the protein, including part of the Biotinyl protein ligase and lipoyl protein ligase, catalytic domain (IPR004143). The variant allele was found at a frequency of 6.4e-05 in 1609808 control chromosomes (gnomAD v4.0.0). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.368delA in individuals affected with Lipoyl Transferase 1 Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have reported clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Mar 30, 2024

ClinVar Genomic variation as it relates to human health

NM_145199.3(LIPT1):c.368del (p.Lys123fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...