This variant is present in population databases (rs770287341, gnomAD 0.008%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 581 of the ABCD4 protein (p.Ser581Arg). This variant has not been reported in the literature in individuals affected with ABCD4-related conditions. 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ABCD4 protein function.
ClinVar Genomic variation as it relates to human health
NM_005050.4(ABCD4):c.1743C>G (p.Ser581Arg)
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.
(1)
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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.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_005050.4(ABCD4):c.1743C>G (p.Ser581Arg)
Variation ID: 2198918 Accession: VCV002198918.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 14q24.3 14: 74286710 (GRCh38) [ NCBI UCSC ] 14: 74753413 (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 Feb 8, 2023 Feb 14, 2024 Jun 13, 2022 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_005050.4:c.1743C>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_005041.1:p.Ser581Arg missense NM_001353591.2:c.1617C>G NP_001340520.1:p.Ser539Arg missense NM_001353592.2:c.1617C>G NP_001340521.1:p.Ser539Arg missense NM_001353593.2:c.1482C>G NP_001340522.1:p.Ser494Arg missense NM_001353594.2:c.1431C>G NP_001340523.1:p.Ser477Arg missense NM_001353595.2:c.1329C>G NP_001340524.1:p.Ser443Arg missense NM_001353596.2:c.1329C>G NP_001340525.1:p.Ser443Arg missense NM_001353597.2:c.1278C>G NP_001340526.1:p.Ser426Arg missense NM_001353598.2:c.1266C>G NP_001340527.1:p.Ser422Arg missense NM_001353599.2:c.1266C>G NP_001340528.1:p.Ser422Arg missense NM_001353600.2:c.1266C>G NP_001340529.1:p.Ser422Arg missense NM_001353601.2:c.1266C>G NP_001340530.1:p.Ser422Arg missense NM_001353602.2:c.954C>G NP_001340531.1:p.Ser318Arg missense NM_001353603.2:c.954C>G NP_001340532.1:p.Ser318Arg missense NM_001353604.2:c.954C>G NP_001340533.1:p.Ser318Arg missense NM_001353605.2:c.954C>G NP_001340534.1:p.Ser318Arg missense NM_001353606.2:c.954C>G NP_001340535.1:p.Ser318Arg missense NM_001353607.2:c.954C>G NP_001340536.1:p.Ser318Arg missense NM_001353608.2:c.954C>G NP_001340537.1:p.Ser318Arg missense NM_001353609.2:c.954C>G NP_001340538.1:p.Ser318Arg missense NM_001353610.2:c.*80C>G 3 prime UTR NM_020323.1:c.1614C>G NP_064719.1:p.Ser538Arg missense NM_020324.3:c.1266C>G NP_064720.1:p.Ser422Arg missense NM_020325.3:c.1743C>G NP_064730.1:p.Ser581Arg missense NR_003256.3:n.1637C>G non-coding transcript variant NR_148466.2:n.1573C>G non-coding transcript variant NR_148467.2:n.1354C>G non-coding transcript variant NR_148468.2:n.1331C>G non-coding transcript variant NR_148469.2:n.1578C>G non-coding transcript variant NR_148470.2:n.1540C>G non-coding transcript variant NR_148471.2:n.1578C>G non-coding transcript variant NR_148472.2:n.1627C>G non-coding transcript variant NR_148473.2:n.1554C>G non-coding transcript variant NR_148474.2:n.1673C>G non-coding transcript variant NC_000014.9:g.74286710G>C NC_000014.8:g.74753413G>C NG_032875.1:g.21355C>G - Protein change
- S318R, S426R, S477R, S494R, S581R, S422R, S538R, S539R, S443R
- Other names
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- Canonical SPDI
- NC_000014.9:74286709:G:C
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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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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
Help
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
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. |
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| ABCD4 | - | - |
GRCh38 GRCh37 |
430 | 452 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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Jun 13, 2022 | RCV002633980.3 |
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. |
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Uncertain significance
(Jun 13, 2022)
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criteria provided, single submitter
Method: clinical testing
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Methylmalonic acidemia with homocystinuria, type cblJ
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003520185.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 14, 2024 |
Comment:
This variant is present in population databases (rs770287341, gnomAD 0.008%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic … (more)
This variant is present in population databases (rs770287341, gnomAD 0.008%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 581 of the ABCD4 protein (p.Ser581Arg). This variant has not been reported in the literature in individuals affected with ABCD4-related conditions. 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ABCD4 protein function. (less)
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Comment:
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:
This variant is present in population databases (rs770287341, gnomAD 0.008%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 581 of the ABCD4 protein (p.Ser581Arg). This variant has not been reported in the literature in individuals affected with ABCD4-related conditions. 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ABCD4 protein function.
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 this variant ...
HelpRecord last updated Sep 29, 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.