This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 339 of the SULF1 protein (p.Arg339His). This variant is present in population databases (rs61747207, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with SULF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2509363). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.
ClinVar Genomic variation as it relates to human health
NM_001128205.2(SULF1):c.1016G>A (p.Arg339His)
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.
(2)
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.
Uncertain significance
2
criteria provided, multiple submitters, no conflicts
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001128205.2(SULF1):c.1016G>A (p.Arg339His)
Variation ID: 2509363 Accession: VCV002509363.3
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 8q13.3 8: 69601784 (GRCh38) [ NCBI UCSC ] 8: 70514019 (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 Jul 8, 2023 May 1, 2024 Sep 11, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001128205.2:c.1016G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001121677.1:p.Arg339His missense NM_001128204.2:c.1016G>A NP_001121676.1:p.Arg339His missense NM_001128206.2:c.1016G>A NP_001121678.1:p.Arg339His missense NM_001412828.1:c.1016G>A NP_001399757.1:p.Arg339His missense NM_001412829.1:c.1016G>A NP_001399758.1:p.Arg339His missense NM_001412830.1:c.1016G>A NP_001399759.1:p.Arg339His missense NM_001412831.1:c.1016G>A NP_001399760.1:p.Arg339His missense NM_001412832.1:c.1016G>A NP_001399761.1:p.Arg339His missense NM_001412833.1:c.1016G>A NP_001399762.1:p.Arg339His missense NM_001412834.1:c.1016G>A NP_001399763.1:p.Arg339His missense NM_001412835.1:c.1016G>A NP_001399764.1:p.Arg339His missense NM_001412836.1:c.1016G>A NP_001399765.1:p.Arg339His missense NM_001412837.1:c.1016G>A NP_001399766.1:p.Arg339His missense NM_001412838.1:c.1016G>A NP_001399767.1:p.Arg339His missense NM_001412839.1:c.1016G>A NP_001399768.1:p.Arg339His missense NM_001412840.1:c.1016G>A NP_001399769.1:p.Arg339His missense NM_001412841.1:c.830G>A NP_001399770.1:p.Arg277His missense NM_001412842.1:c.830G>A NP_001399771.1:p.Arg277His missense NM_001412843.1:c.1016G>A NP_001399772.1:p.Arg339His missense NM_001412844.1:c.416G>A NP_001399773.1:p.Arg139His missense NM_001412845.1:c.416G>A NP_001399774.1:p.Arg139His missense NM_001412846.1:c.-760G>A 5 prime UTR NM_001412847.1:c.1016G>A NP_001399776.1:p.Arg339His missense NM_001412848.1:c.1016G>A NP_001399777.1:p.Arg339His missense NM_001412849.1:c.1016G>A NP_001399778.1:p.Arg339His missense NM_001412850.1:c.1016G>A NP_001399779.1:p.Arg339His missense NM_001412851.1:c.1016G>A NP_001399780.1:p.Arg339His missense NM_015170.3:c.1016G>A NP_055985.2:p.Arg339His missense NR_132437.1:n.366G>A non-coding transcript variant NR_156414.2:n.1523G>A non-coding transcript variant NR_156415.2:n.1685G>A non-coding transcript variant NR_182050.1:n.1414G>A non-coding transcript variant NR_182051.1:n.1576G>A non-coding transcript variant NR_182053.1:n.1576G>A non-coding transcript variant NR_182055.1:n.1154G>A non-coding transcript variant NC_000008.11:g.69601784G>A NC_000008.10:g.70514019G>A NG_042849.1:g.140161G>A - Protein change
- R277H, R339H, R139H
- Other names
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- Canonical SPDI
- NC_000008.11:69601783:G:A
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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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| SULF1 | - | - |
GRCh38 GRCh37 |
306 | 340 | |
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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Sep 11, 2023 | RCV003561262.2 | |
| Uncertain significance (1) |
criteria provided, single submitter
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Mar 17, 2023 | RCV004284027.1 |
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
(Sep 11, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004277417.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 339 of the SULF1 protein (p.Arg339His). … (more)
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 339 of the SULF1 protein (p.Arg339His). This variant is present in population databases (rs61747207, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with SULF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2509363). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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. (less)
|
|
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Uncertain significance
(Mar 17, 2023)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV003940061.2
First in ClinVar: Jul 08, 2023 Last updated: May 01, 2024 |
Comment:
The c.1016G>A (p.R339H) alteration is located in exon 10 (coding exon 6) of the SULF1 gene. This alteration results from a G to A substitution … (more)
The c.1016G>A (p.R339H) alteration is located in exon 10 (coding exon 6) of the SULF1 gene. This alteration results from a G to A substitution at nucleotide position 1016, causing the arginine (R) at amino acid position 339 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
|
Comment:
Comment:
The c.1016G>A (p.R339H) alteration is located in exon 10 (coding exon 6) of the SULF1 gene. This alteration results from a G to A substitution at nucleotide position 1016, causing the arginine (R) at amino acid position 339 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
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 sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 339 of the SULF1 protein (p.Arg339His). This variant is present in population databases (rs61747207, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with SULF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2509363). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.
Comment:
The c.1016G>A (p.R339H) alteration is located in exon 10 (coding exon 6) of the SULF1 gene. This alteration results from a G to A substitution at nucleotide position 1016, causing the arginine (R) at amino acid position 339 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
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 Nov 10, 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.