ClinVar Genomic variation as it relates to human health
NM_013386.5(SLC25A24):c.650G>A (p.Arg217His)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_013386.5(SLC25A24):c.650G>A (p.Arg217His)
Variation ID: 370032 Accession: VCV000370032.11
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1p13.3 1: 108157481 (GRCh38) [ NCBI UCSC ] 1: 108700103 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Oct 19, 2017 Sep 29, 2024 Jun 6, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_013386.5:c.650G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_037518.3:p.Arg217His missense NM_213651.3:c.593G>A NP_998816.1:p.Arg198His missense NC_000001.11:g.108157481C>T NC_000001.10:g.108700103C>T NG_032752.1:g.47878G>A - Protein change
- R198H, R217H
- Other names
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- Canonical SPDI
- NC_000001.11:108157480:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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variation affecting protein; Variation Ontology [ VariO:0002]
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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.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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. |
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SLC25A24 | - | - |
GRCh38 GRCh38 GRCh37 |
126 | 157 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Oct 31, 2018 | RCV000508607.6 | |
Pathogenic (4) |
criteria provided, single submitter
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Jun 6, 2024 | RCV001249454.7 |
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
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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
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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. |
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Pathogenic
(Oct 04, 2016)
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criteria provided, single submitter
Method: clinical testing
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Fontaine progeroid syndrome
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV000320993.1
First in ClinVar: Oct 19, 2017 Last updated: Oct 19, 2017 |
Comment:
The variant was identified as de novo in three independent cases with the syndrome and functional studies have shown a likely altered function of the … (more)
The variant was identified as de novo in three independent cases with the syndrome and functional studies have shown a likely altered function of the protein. (less)
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Pathogenic
(Oct 31, 2018)
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criteria provided, single submitter
Method: clinical testing
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Fontaine progeroid syndrome
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000893168.1
First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019 |
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Pathogenic
(Jun 06, 2024)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV002097451.3
First in ClinVar: Feb 20, 2022 Last updated: Sep 29, 2024 |
Comment:
Published functional studies suggest that this variant results in mitochondrial dysfunction (PMID: 29100093, 29100094); Not observed at significant frequency in large population cohorts (gnomAD); This … (more)
Published functional studies suggest that this variant results in mitochondrial dysfunction (PMID: 29100093, 29100094); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 30329211, 30281880, 29100093, 29100094, 21216154, 19731360, 10594888, 31775791, 31231135, 36093452, Pannier2022[Abstract], 37449547, 36647814) (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV002035623.1 First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV002037414.1 First in ClinVar: Dec 21, 2021 Last updated: Dec 21, 2021 |
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Pathogenic
(Oct 11, 2022)
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no assertion criteria provided
Method: literature only
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FONTAINE PROGEROID SYNDROME
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000679988.2
First in ClinVar: Jan 29, 2018 Last updated: Oct 15, 2022 |
Comment on evidence:
In 4 unrelated girls with Fontaine progeroid syndrome (FPS; 612289), including a Hungarian girl originally reported by Adolphs et al. (2011), Ehmke et al. (2017) … (more)
In 4 unrelated girls with Fontaine progeroid syndrome (FPS; 612289), including a Hungarian girl originally reported by Adolphs et al. (2011), Ehmke et al. (2017) identified heterozygosity for a de novo c.650G-A transition (c.650G-A, NM_013386.4) in exon 5 of the SLC25A24 gene, resulting in an arg217-to-his (R217H) substitution at a highly conserved residue in the predicted helix 1 of the transmembrane domain. The mutation was not found in the ExAC, gnomAD, or 1000 Genomes Project databases. Skin fibroblasts from 2 of the patients (patients 1 and 4) showed mitochondrial swelling, which developed into ballooning after induction of oxidative stress by treatment with H2O2, whereas control fibroblasts appeared almost unchanged; these findings were corroborated by transmission electron microscopy. In transfected HeLa cells, wildtype and mutant proteins both localized to mitochondria, but there was mitochondrial swelling and increased fragmentation with the mutant, which was more pronounced after treatment with H2O2. The mitochondrial membrane potential (MMP) showed no abnormality in patient fibroblasts under normal conditions; however, after treatment with H2O2, the MMP appeared higher in mutant fibroblasts than in control cells, indicating an altered proton gradient. Analysis of the ATP content of the mitochondrial matrix using firefly luciferase, an ATP-dependent enzyme, showed that patient fibroblasts had reduced firefly activity, consistent with a reduced matrix ATP content. Three of the patients were alive at ages 5, 5.5, and 7 years at last exam, but 1 patient (patient 4), a Turkish girl, died at age 20 months from a urinary tract infection. In 3 unrelated infants with FPS, including a Slovenian male infant (patient 1), a French female infant (patient 2) originally reported by Faivre et al. (1999), and an Italian male newborn (patient 4) previously described by Castori et al. (2009), Writzl et al. (2017) identified heterozygosity for the R217H mutation in SLC25A24, at a residue located just below the m-gate of the carrier, within the fully conserved mitochondrial carrier family (MCF) signature. The mutation was not found in the Slovenian exome database or the dbSNP (build 141), gnomAD, GoNL, or UK10K databases. Patient fibroblasts showed localization of the mutant protein to mitochondria, which were enlarged and swollen close to the nucleus; electron microscopy revealed abnormal cristae, which were larger and more dense in the swollen mitochondria than in normal mitochondria. Overexpression of the R217H mutant in HeLa and COS-7 cells showed abnormal swollen mitochondria similar to those observed in patient fibroblasts; however, in contrast to patient fibroblasts, the entire mitochondrial network appeared homogeneously affected. The Italian male newborn died at 20 hours of life from respiratory distress, and the other 2 patients died at 6 months and 7 months of age, from pulmonary hypertension and sepsis, respectively. (less)
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not provided
(-)
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no classification provided
Method: phenotyping only
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Not Provided
Affected status: unknown
Allele origin:
unknown
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GenomeConnect, ClinGen
Accession: SCV001423466.1
First in ClinVar: Jul 19, 2020 Last updated: Jul 19, 2020 |
Comment:
Variant interpretted as Uncertain significance and reported on 08-17-2017 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the … (more)
Variant interpretted as Uncertain significance and reported on 08-17-2017 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. (less)
Clinical Features:
Abnormality of the amniotic fluid (present) , Premature birth (present) , Abnormality of the umbilical cord (present) , Hemihypertrophy (present) , Short stature (present) , … (more)
Abnormality of the amniotic fluid (present) , Premature birth (present) , Abnormality of the umbilical cord (present) , Hemihypertrophy (present) , Short stature (present) , Failure to thrive (present) , Abnormality of the chin (present) , Abnormal facial shape (present) , Abnormality of the hair (present) , Abnormality of the oral cavity (present) , Abnormality of the skull (present) , Abnormality of eye movement (present) , Abnormality of vision (present) , Ear malformation (present) , Conductive hearing impairment (present) , Hyperhidrosis (present) , Abnormality of limb bone morphology (present) , Abnormality of digit (present) , Abnormality of cardiovascular system morphology (present) , Feeding difficulties (present) , Abnormality of the urethra (present) , Abnormality of primary teeth (present) (less)
Indication for testing: Diagnostic
Age: 0-9 years
Sex: male
Testing laboratory: GeneDx
Date variant was reported to submitter: 2017-08-17
Testing laboratory interpretation: Uncertain significance
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Germline Functional Evidence
Functional
Help
The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence |
Method
Help
A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter. |
Result
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A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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variation affecting protein
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV000320993.1
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Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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De Novo Mutations in SLC25A24 Cause a Disorder Characterized by Early Aging, Bone Dysplasia, Characteristic Face, and Early Demise. | Writzl K | American journal of human genetics | 2017 | PMID: 29100094 |
De Novo Mutations in SLC25A24 Cause a Craniosynostosis Syndrome with Hypertrichosis, Progeroid Appearance, and Mitochondrial Dysfunction. | Ehmke N | American journal of human genetics | 2017 | PMID: 29100093 |
Necrotizing soft tissue infection of the scalp after fronto-facial advancement by internal distraction in a 7-year old girl with Gorlin-Chaudhry-Moss syndrome--a case report. | Adolphs N | Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery | 2011 | PMID: 21216154 |
Fontaine-Farriaux syndrome: a recognizable craniosynostosis syndrome with nail, skeletal, abdominal, and central nervous system anomalies. | Castori M | American journal of medical genetics. Part A | 2009 | PMID: 19731360 |
Can Hutchinson-Gilford progeria syndrome be a neonatal condition? | Faivre L | American journal of medical genetics | 1999 | PMID: 10594888 |
Text-mined citations for rs1553253989 ...
HelpRecord last updated Oct 08, 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.