NM_017951.5(SMPD4):c.1174del (p.Ala392fs) AND Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 25, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003151858.2

Allele description [Variation Report for NM_017951.5(SMPD4):c.1174del (p.Ala392fs)]

NM_017951.5(SMPD4):c.1174del (p.Ala392fs)

Gene:

SMPD4:sphingomyelin phosphodiesterase 4 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q21.1

Genomic location:

Preferred name:

NM_017951.5(SMPD4):c.1174del (p.Ala392fs)

HGVS:

NC_000002.12:g.130156599del
NG_053070.1:g.31152del
NM_001171083.2:c.985del
NM_017751.4:c.1204del
NM_017951.5:c.1174delMANE SELECT
NP_001164554.1:p.Ala329fs
NP_060221.2:p.Ala402fs
NP_060421.3:p.Ala392fs
NC_000002.11:g.130914172del
NM_017951.4:c.1291del
NR_033231.3:n.1149del
NR_033232.3:n.1129del

Protein change:

A329fs

Links:

dbSNP: rs2104814089

NCBI 1000 Genomes Browser:

rs2104814089

Molecular consequence:

NM_001171083.2:c.985del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_017751.4:c.1204del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_017951.5:c.1174del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_033231.3:n.1149del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_033232.3:n.1129del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
Identifiers:: MONDO: MONDO:0032838; MedGen: C5231431; OMIM: 618622

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003840277	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 25, 2020)	biparental	research	PubMed (2) [See all records that cite these PMIDs] 25741868, 31495489

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003840277

Equipe Genetique des Anomalies du Developpement, Université de Bourgogne

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 25, 2020)

biparental

research

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	biparental	yes	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Loss of SMPD4 Causes a Developmental Disorder Characterized by Microcephaly and Congenital Arthrogryposis.

Magini P, Smits DJ, Vandervore L, Schot R, Columbaro M, Kasteleijn E, van der Ent M, Palombo F, Lequin MH, Dremmen M, de Wit MCY, Severino M, Divizia MT, Striano P, Ordonez-Herrera N, Alhashem A, Al Fares A, Al Ghamdi M, Rolfs A, Bauer P, Demmers J, Verheijen FW, et al.

Am J Hum Genet. 2019 Oct 3;105(4):689-705. doi: 10.1016/j.ajhg.2019.08.006. Epub 2019 Sep 5.

PubMed [citation]

PMID:: 31495489
PMCID:: PMC6817560

Details of each submission

From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV003840277.1

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

Description

This variant was observed in compound heterozygosity with variant c.1257_1259del

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

Last Updated: Sep 16, 2024

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