NM_017668.3(NDE1):c.872C>T (p.Ser291Phe) AND Lissencephaly 4

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Sep 1, 2017
Review status:: criteria provided, conflicting classifications

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:: RCV000146502.19

Allele description [Variation Report for NM_017668.3(NDE1):c.872C>T (p.Ser291Phe)]

NM_017668.3(NDE1):c.872C>T (p.Ser291Phe)

Gene:

NDE1:nudE neurodevelopment protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.11

Genomic location:

Preferred name:

NM_017668.3(NDE1):c.872C>T (p.Ser291Phe)

HGVS:

NC_000016.10:g.15696785C>T
NG_021210.1:g.58519C>T
NM_001143979.2:c.872C>T
NM_017668.3:c.872C>TMANE SELECT
NP_001137451.1:p.Ser291Phe
NP_060138.1:p.Ser291Phe
NC_000016.9:g.15790642C>T
NM_001143979.1:c.872C>T

Protein change:

S291F

Links:

dbSNP: rs146284370

NCBI 1000 Genomes Browser:

rs146284370

Molecular consequence:

NM_001143979.2:c.872C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_017668.3:c.872C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Lissencephaly 4 (LIS4)
Synonyms:: Lissencephaly 4 (with microcephaly)
Identifiers:: MONDO: MONDO:0013527; MedGen: C3151461; Orphanet: 1083; OMIM: 614019

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000193792	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Uncertain significance (Feb 17, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000807611	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 1, 2017)	maternal	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 25326635
SCV001277270	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000193792

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2007)

Uncertain significance
(Feb 17, 2014)

germline

clinical testing

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

SCV000807611

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 1, 2017)

maternal

clinical testing

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

SCV001277270

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee.

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

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

See all PubMed Citations (3)

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000193792.1

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV000807611.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing (GTR000508680.4)	PubMed (2)

Description

Likely pathogenicity based on finding it once in our laboratory in trans with a 16p13.11 deletion in a 1-year-old male with global delays, hypotonia, poor weight gain, optic atrophy, abnormal auditory brainstem responses, strabismus, brachycephaly. Heterozygotes are expected to be asymptomatic carriers.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided	(GTR000508680.4)	not provided	not provided	not provided	not provided

From Illumina Laboratory Services, Illumina, SCV001277270.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

Last Updated: Nov 24, 2024

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