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NM_000543.5(SMPD1):c.107_116delinsCGC (p.Val36fs) AND SMPD1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 5, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV004743247.1

Allele description [Variation Report for NM_000543.5(SMPD1):c.107_116delinsCGC (p.Val36fs)]

NM_000543.5(SMPD1):c.107_116delinsCGC (p.Val36fs)

Gene:
SMPD1:sphingomyelin phosphodiesterase 1 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_000543.5(SMPD1):c.107_116delinsCGC (p.Val36fs)
HGVS:
  • NC_000011.10:g.6390705_6390714delinsCGC
  • NG_011780.1:g.5281_5290delinsCGC
  • NM_000543.5:c.107_116delinsCGCMANE SELECT
  • NM_001007593.3:c.107_116delinsCGC
  • NM_001318087.2:c.107_116delinsCGC
  • NM_001318088.2:c.-855_-846delinsCGC
  • NM_001365135.2:c.107_116delinsCGC
  • NP_000534.3:p.Val36fs
  • NP_001007594.2:p.Val36fs
  • NP_001305016.1:p.Val36fs
  • NP_001352064.1:p.Val36fs
  • NC_000011.9:g.6411935_6411944delinsCGC
  • NM_000543.4:c.107_116delinsCGC
  • NR_027400.3:n.232_241delinsCGC
  • NR_134502.2:n.232_241delinsCGC
Protein change:
V36fs
Links:
dbSNP: rs1590735307
NCBI 1000 Genomes Browser:
rs1590735307
Molecular consequence:
  • NM_001318088.2:c.-855_-846delinsCGC - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000543.5:c.107_116delinsCGC - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001007593.3:c.107_116delinsCGC - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001318087.2:c.107_116delinsCGC - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001365135.2:c.107_116delinsCGC - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_027400.3:n.232_241delinsCGC - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_134502.2:n.232_241delinsCGC - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
SMPD1-related disorder
Synonyms:
SMPD1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005366672PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Aug 5, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005366672.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The SMPD1 c.107_116delinsCGC variant is predicted to result in a frameshift and premature protein termination (p.Val36Alafs*39). To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. Frameshift variants in SMPD1 are expected to be pathogenic. This variant is interpreted as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024