Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
ClinVar Genomic variation as it relates to human health
NM_153816.6(SNX14):c.2654A>G (p.Asp885Gly)
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, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_153816.6(SNX14):c.2654A>G (p.Asp885Gly)
Variation ID: 2501981 Accession: VCV002501981.2
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 6q14.3 6: 85508059 (GRCh38) [ NCBI UCSC ] 6: 86217777 (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 20, 2023 Mar 30, 2024 May 10, 2023 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_153816.6:c.2654A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_722523.1:p.Asp885Gly missense NM_001297614.3:c.2627A>G NP_001284543.1:p.Asp876Gly missense NM_001304479.2:c.2498A>G NP_001291408.1:p.Asp833Gly missense NM_001350532.2:c.2717A>G NP_001337461.1:p.Asp906Gly missense NM_001350533.2:c.2651A>G NP_001337462.1:p.Asp884Gly missense NM_001350534.2:c.2624A>G NP_001337463.1:p.Asp875Gly missense NM_001350535.2:c.2651A>G NP_001337464.1:p.Asp884Gly missense NM_001350536.2:c.2522A>G NP_001337465.1:p.Asp841Gly missense NM_001350537.2:c.2519A>G NP_001337466.1:p.Asp840Gly missense NM_001350538.2:c.2510A>G NP_001337467.1:p.Asp837Gly missense NM_001350539.2:c.2495A>G NP_001337468.1:p.Asp832Gly missense NM_001350540.2:c.2489A>G NP_001337469.1:p.Asp830Gly missense NM_001350541.2:c.2462A>G NP_001337470.1:p.Asp821Gly missense NM_001350542.2:c.2366A>G NP_001337471.1:p.Asp789Gly missense NM_001350543.2:c.2363A>G NP_001337472.1:p.Asp788Gly missense NM_001350544.2:c.2354A>G NP_001337473.1:p.Asp785Gly missense NM_001350545.2:c.2210A>G NP_001337474.1:p.Asp737Gly missense NM_001350546.2:c.2210A>G NP_001337475.1:p.Asp737Gly missense NM_001350547.2:c.1604A>G NP_001337476.1:p.Asp535Gly missense NM_001350548.2:c.1499A>G NP_001337477.1:p.Asp500Gly missense NM_001350549.2:c.1499A>G NP_001337478.1:p.Asp500Gly missense NM_001350550.2:c.1499A>G NP_001337479.1:p.Asp500Gly missense NM_001350551.2:c.1499A>G NP_001337480.1:p.Asp500Gly missense NM_001350552.2:c.1499A>G NP_001337481.1:p.Asp500Gly missense NM_001350553.2:c.1472A>G NP_001337482.1:p.Asp491Gly missense NM_020468.6:c.2495A>G NP_065201.1:p.Asp832Gly missense NR_146774.2:n.2790A>G non-coding transcript variant NR_146775.2:n.2793A>G non-coding transcript variant NR_146776.2:n.2916A>G non-coding transcript variant NR_146777.2:n.3044A>G non-coding transcript variant NR_146778.2:n.3048A>G non-coding transcript variant NR_146779.2:n.3045A>G non-coding transcript variant NC_000006.12:g.85508059T>C NC_000006.11:g.86217777T>C NG_047171.1:g.91098A>G - Protein change
- D491G, D500G, D535G, D737G, D785G, D788G, D789G, D821G, D830G, D832G, D833G, D837G, D840G, D841G, D875G, D876G, D884G, D885G, D906G
- Other names
- -
- Canonical SPDI
- NC_000006.12:85508058:T:C
-
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.
- -
- 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. |
|||
| SNX14 | - | - |
GRCh38 GRCh37 |
287 | 309 | |
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 (2) |
criteria provided, single submitter
|
May 10, 2023 | RCV003228400.10 |
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
(May 10, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV003924745.1
First in ClinVar: May 20, 2023 Last updated: May 20, 2023 |
Comment:
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not … (more)
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge (less)
|
|
|
not provided
(-)
|
no classification provided
Method: phenotyping only
|
not provided
Affected status: unknown
Allele origin:
unknown
|
GenomeConnect - Brain Gene Registry
Accession: SCV004804635.1
First in ClinVar: Mar 30, 2024 Last updated: Mar 30, 2024 |
Comment:
Variant classified as Uncertain significance and reported on 01-06-2022 by GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect … (more)
Variant classified as Uncertain significance and reported on 01-06-2022 by GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. (less)
Clinical Features:
Macrocephaly (present)
Indication for testing: Diagnostic
Age: 0-9 years
Sex: male
Method: Exome Sequencing
Testing laboratory: GeneDx
Date variant was reported to submitter: 2022-01-06
Testing laboratory interpretation: Uncertain significance
|
Comment:
Comment:
Variant classified as Uncertain significance and reported on 01-06-2022 by GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.
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:
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Comment:
Variant classified as Uncertain significance and reported on 01-06-2022 by GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.
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 Jul 15, 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.