NM_000018.4(ACADVL):c.62+21_62+28del AND Very long chain acyl-CoA dehydrogenase deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 4, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003811712.1

Allele description

NM_000018.4(ACADVL):c.62+21_62+28del

Genes:

LOC130060113:ATAC-STARR-seq lymphoblastoid silent region 8088 [Gene]
ACADVL:acyl-CoA dehydrogenase very long chain [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000018.4(ACADVL):c.62+21_62+28del

HGVS:

NC_000017.11:g.7220067_7220074del
NG_007975.1:g.5234_5241del
NG_008391.2:g.4980_4987del
NG_008391.3:g.4979_4986del
NG_194534.1:g.106_113del
NM_000018.4:c.62+21_62+28delMANE SELECT
NM_001033859.3:c.62+21_62+28del
NM_001270447.2:c.132-55_132-48del
NM_001270448.2:c.-221_-214del
NC_000017.10:g.7123383_7123390del
NC_000017.10:g.7123386_7123393del

Molecular consequence:

NM_001270448.2:c.-221_-214del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000018.4:c.62+21_62+28del - intron variant - [Sequence Ontology: SO:0001627]
NM_001033859.3:c.62+21_62+28del - intron variant - [Sequence Ontology: SO:0001627]
NM_001270447.2:c.132-55_132-48del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Very long chain acyl-CoA dehydrogenase deficiency (ACADVLD)
Synonyms:: VLCAD deficiency
Identifiers:: MONDO: MONDO:0008723; MedGen: C3887523; Orphanet: 26793; OMIM: 201475

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Cusickiella douglasii voucher E. Schranz 1072 Dpa1 gene, partial sequence
Cusickiella douglasii voucher E. Schranz 1072 Dpa1 gene, partial sequence
gi|401018505|gb|JX146866.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004616176	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Aug 4, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004616176

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Aug 4, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004616176.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change falls in intron 1 of the ACADVL gene. It does not directly change the encoded amino acid sequence of the ACADVL protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with ACADVL-related conditions (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 5, 2024

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