NM_000543.5(SMPD1):c.1101dup (p.Phe368fs) AND Niemann-Pick disease, type A

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Mar 11, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000668954.2

Allele description [Variation Report for NM_000543.5(SMPD1):c.1101dup (p.Phe368fs)]

NM_000543.5(SMPD1):c.1101dup (p.Phe368fs)

Gene:

SMPD1:sphingomyelin phosphodiesterase 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000543.5(SMPD1):c.1101dup (p.Phe368fs)

Other names:

p.Phe368ValfsTer23

HGVS:

NC_000011.10:g.6393225dup
NG_011780.1:g.7801dup
NG_029615.1:g.31195dup
NM_000543.5:c.1101dupMANE SELECT
NM_001007593.3:c.1098dup
NM_001318087.2:c.1101dup
NM_001318088.2:c.180dup
NM_001365135.2:c.1132-392dup
NP_000534.3:p.Phe368fs
NP_001007594.2:p.Phe367fs
NP_001305016.1:p.Phe368fs
NP_001305017.1:p.Phe61fs
NC_000011.9:g.6414449_6414450insG
NC_000011.9:g.6414455dup
NM_000543.4:c.1101dupG
NR_134502.2:n.573dup

Protein change:

F367fs

Links:

dbSNP: rs1422720020

NCBI 1000 Genomes Browser:

rs1422720020

Molecular consequence:

NM_000543.5:c.1101dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001007593.3:c.1098dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318087.2:c.1101dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318088.2:c.180dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365135.2:c.1132-392dup - intron variant - [Sequence Ontology: SO:0001627]
NR_134502.2:n.573dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Functional consequence:

loss_of_function_variant [Sequence Ontology: SO:0002054]

Condition(s)

Name:: Niemann-Pick disease, type A
Synonyms:: SPHINGOMYELIN LIPIDOSIS; SPHINGOMYELINASE DEFICIENCY
Identifiers:: MONDO: MONDO:0009756; MedGen: C0268242; Orphanet: 77292; OMIM: 257200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000793638	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Aug 31, 2017)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23356216, 27338287 Citation Link,
SCV005052841	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 11, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000793638

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(Aug 31, 2017)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV005052841

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 11, 2024)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of a distinct mutation spectrum in the SMPD1 gene of Chinese patients with acid sphingomyelinase-deficient Niemann-Pick disease.

Zhang H, Wang Y, Gong Z, Li X, Qiu W, Han L, Ye J, Gu X.

Orphanet J Rare Dis. 2013 Jan 28;8:15. doi: 10.1186/1750-1172-8-15.

PubMed [citation]

PMID:: 23356216
PMCID:: PMC3566977

Spectrum of SMPD1 mutations in Asian-Indian patients with acid sphingomyelinase (ASM)-deficient Niemann-Pick disease.

Ranganath P, Matta D, Bhavani GS, Wangnekar S, Jain JM, Verma IC, Kabra M, Puri RD, Danda S, Gupta N, Girisha KM, Sankar VH, Patil SJ, Ramadevi AR, Bhat M, Gowrishankar K, Mandal K, Aggarwal S, Tamhankar PM, Tilak P, Phadke SR, Dalal A.

Am J Med Genet A. 2016 Oct;170(10):2719-30. doi: 10.1002/ajmg.a.37817. Epub 2016 Jun 24.

PubMed [citation]

PMID:: 27338287

See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000793638.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV005052841.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 17, 2024

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