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NM_000543.5(SMPD1):c.1763C>T (p.Thr588Met)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000235264.8
Variation ID:
235264
Description:
single nucleotide variant
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NM_000543.5(SMPD1):c.1763C>T (p.Thr588Met)

Allele ID
236951
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.4
Genomic location
11: 6394474 (GRCh38) GRCh38 UCSC
11: 6415704 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.6394474C>T
NC_000011.9:g.6415704C>T
NG_011780.1:g.9050C>T
... more HGVS
Protein change
T588M, T281M, T587M, T544M
Other names
-
Canonical SPDI
NC_000011.10:6394473:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.01617 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.01214
Trans-Omics for Precision Medicine (TOPMed) 0.01581
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01555
1000 Genomes Project 0.01617
Links
ClinGen: CA5852983
dbSNP: rs35785620
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jun 13, 2018 RCV000224009.5
Benign 2 criteria provided, multiple submitters, no conflicts Jun 4, 2018 RCV000344652.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000366169.2
Benign 1 criteria provided, single submitter Dec 5, 2020 RCV001081400.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SMPD1 - - GRCh38
GRCh37
582 605

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely Benign
(Aug 25, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000280711.1
Submitted: (May 19, 2016)
Evidence details
Comment:
Converted during submission to Likely benign.
Benign
(May 24, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000342072.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease, type A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000372948.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Jun 04, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000918245.1
Submitted: (Apr 24, 2019)
Evidence details
Comment:
Variant summary: SMPD1 c.1763C>T (p.Thr588Met) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign … (more)
Benign
(Jun 13, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000986309.1
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 05, 2020)
criteria provided, single submitter
Method: clinical testing
Niemann-Pick disease, type B
Niemann-Pick disease, type A
Allele origin: germline
Invitae
Accession: SCV000755901.4
Submitted: (Jan 07, 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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SMPD1 - - - -

Text-mined citations for rs35785620...

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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 Sep 29, 2021