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NM_152264.4(SLC39A13):c.398C>T (p.Thr133Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Oct 23, 2018)
Last evaluated:
Nov 21, 2017
Accession:
VCV000196579.1
Variation ID:
196579
Description:
single nucleotide variant
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NM_152264.4(SLC39A13):c.398C>T (p.Thr133Met)

Allele ID
193740
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p11.2
Genomic location
11: 47412022 (GRCh38) GRCh38 UCSC
11: 47433573 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.47412022C>T
NC_000011.9:g.47433573C>T
NM_001128225.2:c.398C>T NP_001121697.1:p.Thr133Met missense
... more HGVS
Protein change
T133M
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00232
The Genome Aggregation Database (gnomAD), exomes 0.00221
1000 Genomes Project 0.00020
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00254
Trans-Omics for Precision Medicine (TOPMed) 0.00215
Links
dbSNP: rs140574574
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Oct 31, 2017 RCV000488236.4
Uncertain significance 1 criteria provided, single submitter Jan 10, 2014 RCV000415137.1
Likely benign 1 criteria provided, single submitter Nov 17, 2017 RCV000550070.2
Likely benign 1 no assertion criteria provided Nov 21, 2017 RCV000177406.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SLC39A13 - - GRCh38
GRCh37
63 75

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 10, 2014)
criteria provided, single submitter
Method: clinical testing
Abnormality of connective tissue
Abnormality of the skeletal system
Cutis laxa
Mitral valve prolapse
Myopia
Scleroderma
Allele origin: unknown
Centre for Mendelian Genomics,University Medical Centre Ljubljana
Accession: SCV000493054.1
Submitted: (Nov 12, 2016)
Evidence details
Likely benign
(Nov 17, 2017)
criteria provided, single submitter
Method: clinical testing
Spondylocheirodysplasia, Ehlers-Danlos syndrome-like
Allele origin: germline
Invitae
Accession: SCV000646922.2
Submitted: (Apr 02, 2018)
Evidence details
Uncertain significance
(Jan 29, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics
Accession: SCV000229261.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/em...
Uncertain significance
(Oct 31, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000574884.5
Submitted: (Oct 23, 2018)
Evidence details
Likely benign
(Nov 21, 2017)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000525099.4
Submitted: (Mar 26, 2018)
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)

Citations for this variant

Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SLC39A13 - - - -

Record last updated May 28, 2019