The CD36 c.1079T>G (p.Leu360Ter) stop gained variant causes a premature truncation of the protein product. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found with individuals with platelet glycoprotein IV deficiency. This variant is reported at a frequency of 0.001396 in the Other population of the Genome Aggregation Database. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of unknown significance but suspicious for pathogenicity for platelet glycoprotein IV deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
ClinVar Genomic variation as it relates to human health
NM_001001548.3(CD36):c.1079T>G (p.Leu360Ter)
Germline
Classification
Help
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.
(9)
Help
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.
Conflicting classifications of pathogenicity
Pathogenic(5); Likely pathogenic(2); Uncertain significance(1)
Pathogenic(5); Likely pathogenic(2); Uncertain significance(1)
9
criteria provided, conflicting classifications
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001001548.3(CD36):c.1079T>G (p.Leu360Ter)
Variation ID: 632507 Accession: VCV000632507.35
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 7q21.11 7: 80671994 (GRCh38) [ NCBI UCSC ] 7: 80301310 (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 May 27, 2019 Oct 20, 2024 Mar 26, 2024 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001001548.3:c.1079T>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001001548.1:p.Leu360Ter nonsense NM_000072.3:c.1079T>G NP_000063.2:p.Leu360Ter nonsense NM_001001547.3:c.1079T>G NP_001001547.1:p.Leu360Ter nonsense NM_001001548.2:c.1079T>G NM_001127443.1:c.1079T>G NM_001127443.2:c.1079T>G NP_001120915.1:p.Leu360Ter nonsense NM_001127444.2:c.1079T>G NP_001120916.1:p.Leu360Ter nonsense NM_001289908.1:c.962T>G NP_001276837.1:p.Leu321Ter nonsense NM_001289909.1:c.899T>G NP_001276838.1:p.Leu300Ter nonsense NM_001289911.2:c.851T>G NP_001276840.1:p.Leu284Ter nonsense NM_001371074.1:c.1079T>G NP_001358003.1:p.Leu360Ter nonsense NM_001371075.1:c.1079T>G NP_001358004.1:p.Leu360Ter nonsense NM_001371077.1:c.1079T>G NP_001358006.1:p.Leu360Ter nonsense NM_001371078.1:c.1079T>G NP_001358007.1:p.Leu360Ter nonsense NM_001371079.1:c.977T>G NP_001358008.1:p.Leu326Ter nonsense NM_001371080.1:c.614T>G NP_001358009.1:p.Leu205Ter nonsense NM_001371081.1:c.614T>G NP_001358010.1:p.Leu205Ter nonsense NR_110501.1:n.1070T>G non-coding transcript variant NC_000007.14:g.80671994T>G NC_000007.13:g.80301310T>G NG_008192.1:g.74807T>G - Protein change
- L360*, L284*, L321*, L300*, L205*, L326*
- Other names
- -
- Canonical SPDI
- NC_000007.14:80671993:T:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe 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.
-
The Genome Aggregation Database (gnomAD) 0.00017
Trans-Omics for Precision Medicine (TOPMed) 0.00019
Exome Aggregation Consortium (ExAC) 0.00026
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
- Links
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 | ||
|---|---|---|---|---|---|---|
| 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. |
|||
| CD36 | - | - |
GRCh38 GRCh37 |
247 | 270 | |
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. |
|---|---|---|---|---|
| Conflicting interpretations of pathogenicity (7) |
criteria provided, conflicting classifications
|
Mar 26, 2024 | RCV000779539.12 | |
| Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Jul 1, 2023 | RCV001312122.24 |
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
(Dec 03, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Platelet-type bleeding disorder 10
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000916207.1
First in ClinVar: May 27, 2019 Last updated: May 27, 2019 |
Comment:
The CD36 c.1079T>G (p.Leu360Ter) stop gained variant causes a premature truncation of the protein product. A literature search was performed for the gene, cDNA change, … (more)
The CD36 c.1079T>G (p.Leu360Ter) stop gained variant causes a premature truncation of the protein product. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found with individuals with platelet glycoprotein IV deficiency. This variant is reported at a frequency of 0.001396 in the Other population of the Genome Aggregation Database. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of unknown significance but suspicious for pathogenicity for platelet glycoprotein IV deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
|
|
|
Pathogenic
(May 19, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Platelet-type bleeding disorder 10
Affected status: unknown
Allele origin:
unknown
|
Baylor Genetics
Accession: SCV003834966.1
First in ClinVar: Mar 11, 2023 Last updated: Mar 11, 2023 |
|
|
|
Pathogenic
(Jul 04, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Platelet-type bleeding disorder 10
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
inherited
|
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV004027742.1
First in ClinVar: Aug 26, 2023 Last updated: Aug 26, 2023 |
Comment:
Criteria applied: PVS1,PM2_SUP,PM3_SUP
Clinical Features:
Primary microcephaly (present) , Hypotonia (present) , CSF pleocytosis (present) , Generalized-onset seizure (present) , Severe global developmental delay (present) , Delayed myelination (present) , … (more)
Primary microcephaly (present) , Hypotonia (present) , CSF pleocytosis (present) , Generalized-onset seizure (present) , Severe global developmental delay (present) , Delayed myelination (present) , Oral bleeding (present) , Intracranial hemorrhage (present) , Inability to walk (present) , Proximal femoral epiphysiolysis (present) (less)
Sex: female
|
|
|
Likely pathogenic
(Mar 26, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Platelet-type bleeding disorder 10
Affected status: unknown
Allele origin:
germline
|
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004807219.1
First in ClinVar: Apr 06, 2024 Last updated: Apr 06, 2024 |
|
|
|
Likely pathogenic
(-)
|
criteria provided, single submitter
Method: clinical testing
|
Platelet-type bleeding disorder 10
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
|
Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV005073951.1
First in ClinVar: Jul 15, 2024 Last updated: Jul 15, 2024 |
Comment:
The stop gained variant c.1079T>G(p.Leu360Ter) in CD36 gene has been reported in multiple individulas affected with CD36 related disorders (Xu et. al., 2021; Chien et … (more)
The stop gained variant c.1079T>G(p.Leu360Ter) in CD36 gene has been reported in multiple individulas affected with CD36 related disorders (Xu et. al., 2021; Chien et al., 2012; Leprêtre et. al., 2004). The observed variant has allele frequency of 0.02% in gnomAD exomes database. This variant has been submitted to the ClinVar database as Uncertain Significance / Likely Pathogenic / Pathogenic. The nucleotide change c.1079T>G in CD36 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. However, additional functional studies will be required to confirm the pathogenicity of the variant. For these reasons, this variant has been classified as Likely Pathogenic. (less)
|
|
|
Pathogenic
(Jan 08, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Platelet-type bleeding disorder 10
Affected status: yes
Allele origin:
germline
|
Laboratory of Medical Genetics, National & Kapodistrian University of Athens
Accession: SCV005091073.1
First in ClinVar: Aug 04, 2024 Last updated: Aug 04, 2024 |
Comment:
PVS1, PS4, PM2, PP5 - The variant has been reported in ClinVar by other laboratories (Variation ID 632507) and was detected in trans with NM_001127443.1:c.1181_1185dup … (more)
PVS1, PS4, PM2, PP5 - The variant has been reported in ClinVar by other laboratories (Variation ID 632507) and was detected in trans with NM_001127443.1:c.1181_1185dup variant. (less)
|
|
|
Pathogenic
(Jun 12, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Clinical Genetics Laboratory, Skane University Hospital Lund
Accession: SCV005197405.1
First in ClinVar: Aug 25, 2024 Last updated: Aug 25, 2024 |
|
|
|
Pathogenic
(Jul 01, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001502576.23
First in ClinVar: Mar 14, 2021 Last updated: Oct 20, 2024 |
Comment:
CD36: PVS1, PM2
Number of individuals with the variant: 3
|
|
|
Pathogenic
(Oct 30, 2023)
|
no assertion criteria provided
Method: clinical testing
|
Platelet-type bleeding disorder 10
Affected status: yes
Allele origin:
germline
|
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas
Accession: SCV004099449.1
First in ClinVar: Nov 04, 2023 Last updated: Nov 04, 2023 |
|
Comment:
Comment:
Criteria applied: PVS1,PM2_SUP,PM3_SUP
Comment:
The stop gained variant c.1079T>G(p.Leu360Ter) in CD36 gene has been reported in multiple individulas affected with CD36 related disorders (Xu et. al., 2021; Chien et al., 2012; Leprêtre et. al., 2004). The observed variant has allele frequency of 0.02% in gnomAD exomes database. This variant has been submitted to the ClinVar database as Uncertain Significance / Likely Pathogenic / Pathogenic. The nucleotide change c.1079T>G in CD36 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. However, additional functional studies will be required to confirm the pathogenicity of the variant. For these reasons, this variant has been classified as Likely Pathogenic.
Comment:
PVS1, PS4, PM2, PP5 - The variant has been reported in ClinVar by other laboratories (Variation ID 632507) and was detected in trans with NM_001127443.1:c.1181_1185dup variant.
Comment:
CD36: PVS1, PM2
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:
The CD36 c.1079T>G (p.Leu360Ter) stop gained variant causes a premature truncation of the protein product. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found with individuals with platelet glycoprotein IV deficiency. This variant is reported at a frequency of 0.001396 in the Other population of the Genome Aggregation Database. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of unknown significance but suspicious for pathogenicity for platelet glycoprotein IV deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Comment:
Criteria applied: PVS1,PM2_SUP,PM3_SUP
Comment:
The stop gained variant c.1079T>G(p.Leu360Ter) in CD36 gene has been reported in multiple individulas affected with CD36 related disorders (Xu et. al., 2021; Chien et al., 2012; Leprêtre et. al., 2004). The observed variant has allele frequency of 0.02% in gnomAD exomes database. This variant has been submitted to the ClinVar database as Uncertain Significance / Likely Pathogenic / Pathogenic. The nucleotide change c.1079T>G in CD36 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. However, additional functional studies will be required to confirm the pathogenicity of the variant. For these reasons, this variant has been classified as Likely Pathogenic.
Comment:
PVS1, PS4, PM2, PP5 - The variant has been reported in ClinVar by other laboratories (Variation ID 632507) and was detected in trans with NM_001127443.1:c.1181_1185dup variant.
Comment:
CD36: PVS1, PM2
Citations for germline classification of this variant
Help| 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 rs56381858 ...
HelpThese citations are identified by LitVar using
the rs number, so they may include citations for more than one variant
at this location. Please review the LitVar results carefully for your
variant of interest.
Record last updated Oct 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.