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NM_005629.4(SLC6A8):c.92C>T (p.Pro31Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000572616.10
Variation ID:
572616
Description:
single nucleotide variant
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NM_005629.4(SLC6A8):c.92C>T (p.Pro31Leu)

Allele ID
573645
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 153688666 (GRCh38) GRCh38 UCSC
X: 152954121 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.152954121C>T
NC_000023.11:g.153688666C>T
NM_005629.4:c.92C>T MANE Select NP_005620.1:p.Pro31Leu missense
... more HGVS
Protein change
P31L
Other names
-
Canonical SPDI
NC_000023.11:153688665:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00011
Links
dbSNP: rs868950793
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 3, 2020 RCV000694042.4
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Oct 1, 2018 RCV000842126.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SLC6A8 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
470 693

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 30, 2017)
criteria provided, single submitter
Method: curation
Creatine transporter deficiency
Allele origin: unknown
Department of Genetics,Sultan Qaboos University Hospital, Oman
Accession: SCV000891652.1
Submitted: (Oct 25, 2018)
Evidence details
Likely benign
(May 03, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000984122.1
Submitted: (Apr 12, 2019)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Creatine transporter deficiency
Allele origin: germline
Invitae
Accession: SCV000822468.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Oct 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001150478.6
Submitted: (Jul 04, 2021)
Evidence details

Functional evidence

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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.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs868950793...

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These 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 Jul 10, 2021