NM_001876.4(CPT1A):c.1183C>T (p.Arg395Cys) AND Carnitine palmitoyl transferase 1A deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 2021
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:: RCV001364399.6

Allele description [Variation Report for NM_001876.4(CPT1A):c.1183C>T (p.Arg395Cys)]

NM_001876.4(CPT1A):c.1183C>T (p.Arg395Cys)

Genes:

LOC126861244:BRD4-independent group 4 enhancer GRCh37_chr11:68549035-68550234 [Gene]
CPT1A:carnitine palmitoyltransferase 1A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.3

Genomic location:

Preferred name:

NM_001876.4(CPT1A):c.1183C>T (p.Arg395Cys)

HGVS:

NC_000011.10:g.68781940G>A
NG_011801.1:g.64992C>T
NM_001031847.3:c.1183C>T
NM_001876.4:c.1183C>TMANE SELECT
NP_001027017.1:p.Arg395Cys
NP_001867.2:p.Arg395Cys
NC_000011.9:g.68549408G>A

Protein change:

R395C

Links:

dbSNP: rs1451283997

NCBI 1000 Genomes Browser:

rs1451283997

Molecular consequence:

NM_001031847.3:c.1183C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001876.4:c.1183C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Carnitine palmitoyl transferase 1A deficiency
Synonyms:: Carnitine palmitoyl transferase 1 deficiency; Carnitine palmitoyltransferase 1A deficiency; CPT1A deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009705; MedGen: C1829703; Orphanet: 156; OMIM: 255120

Recent activity

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PREDICTED: Rattus norvegicus kelch-like family member 17 (Klhl17), transcript va...
PREDICTED: Rattus norvegicus kelch-like family member 17 (Klhl17), transcript variant X2, mRNA
gi|2678942572|ref|XM_008764336.3|

Nucleotide
Petrosaspongia nigra genomic DNA sequence contains 28S rRNA gene, isolate GW2622...
Petrosaspongia nigra genomic DNA sequence contains 28S rRNA gene, isolate GW26227, specimen voucher QM G304685
gi|1804151137|emb|LR699521.1|

Nucleotide
grainyhead-like protein 3 homolog isoform 1 [Homo sapiens]
grainyhead-like protein 3 homolog isoform 1 [Homo sapiens]
gi|38049007|ref|NP_067003.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001560547	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2021)	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

SCV001560547

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2021)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001560547.3

#	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 replaces arginine with cysteine at codon 395 of the CPT1A protein (p.Arg395Cys). The arginine residue is highly conserved and there is a large physicochemical difference between arginine and cysteine. This variant is not present in population databases (ExAC no frequency). This missense change has been observed in individual(s) with CPT1A-related condition (Invitae). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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