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NM_000019.4(ACAT1):c.233del (p.Lys78fs) AND Deficiency of acetyl-CoA acetyltransferase

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 7, 2020
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:
RCV001385938.5

Allele description [Variation Report for NM_000019.4(ACAT1):c.233del (p.Lys78fs)]

NM_000019.4(ACAT1):c.233del (p.Lys78fs)

Gene:
ACAT1:acetyl-CoA acetyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000019.4(ACAT1):c.233del (p.Lys78fs)
HGVS:
  • NC_000011.10:g.108133932del
  • NG_009888.2:g.22228del
  • NM_000019.4:c.233delMANE SELECT
  • NM_001386677.1:c.233del
  • NM_001386678.1:c.120+1978del
  • NM_001386679.1:c.-45del
  • NM_001386681.1:c.-38del
  • NM_001386682.1:c.-38del
  • NM_001386685.1:c.-38del
  • NM_001386686.1:c.-38del
  • NM_001386687.1:c.-38del
  • NM_001386688.1:c.-38del
  • NM_001386689.1:c.-38del
  • NM_001386690.1:c.-38del
  • NM_001386691.1:c.-38del
  • NP_000010.1:p.Lys78fs
  • NP_001373606.1:p.Lys78fs
  • LRG_1400t1:c.233del
  • LRG_1400:g.22228del
  • LRG_1400p1:p.Lys78fs
  • NC_000011.9:g.108004656del
  • NC_000011.9:g.108004659del
  • NR_170162.1:n.273del
  • NR_170163.1:n.367del
Protein change:
K78fs
Links:
dbSNP: rs2135334849
NCBI 1000 Genomes Browser:
rs2135334849
Molecular consequence:
  • NM_001386679.1:c.-45del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386681.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386682.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386685.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386686.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386687.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386688.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386689.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386690.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001386691.1:c.-38del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000019.4:c.233del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001386677.1:c.233del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001386678.1:c.120+1978del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_170162.1:n.273del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_170163.1:n.367del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Deficiency of acetyl-CoA acetyltransferase
Synonyms:
Alpha-methylacetoaceticaciduria; 2-methyl-3-hydroxybutyricacidemia; Mitochondrial acetoacetyl-CoA Thiolase deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008760; MedGen: C1536500; Orphanet: 134; OMIM: 203750

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001585958Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jul 7, 2020)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Molecular basis of beta-ketothiolase deficiency: mutations and polymorphisms in the human mitochondrial acetoacetyl-coenzyme A thiolase gene.

Fukao T, Yamaguchi S, Orii T, Hashimoto T.

Hum Mutat. 1995;5(2):113-20. Review.

PubMed [citation]
PMID:
7749408

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001585958.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in ACAT1 are known to be pathogenic (PMID: 7749408). This variant has not been reported in the literature in individuals with ACAT1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Lys78Argfs*9) in the ACAT1 gene. It is expected to result in an absent or disrupted protein product.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024