NM_005909.5(MAP1B):c.5368C>T (p.Arg1790Ter) AND Periventricular nodular heterotopia 9

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 23, 2023
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:: RCV003152733.1

Allele description [Variation Report for NM_005909.5(MAP1B):c.5368C>T (p.Arg1790Ter)]

NM_005909.5(MAP1B):c.5368C>T (p.Arg1790Ter)

Gene:

MAP1B:microtubule associated protein 1B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q13.2

Genomic location:

Preferred name:

NM_005909.5(MAP1B):c.5368C>T (p.Arg1790Ter)

HGVS:

NC_000005.10:g.72198723C>T
NM_001324255.2:c.4990C>T
NM_005909.5:c.5368C>TMANE SELECT
NP_001311184.1:p.Arg1664Ter
NP_005900.2:p.Arg1790Ter
NC_000005.9:g.71494550C>T
NM_005909.4:c.5368C>T

Protein change:

R1664*

Links:

dbSNP: rs1580027036

NCBI 1000 Genomes Browser:

rs1580027036

Molecular consequence:

NM_001324255.2:c.4990C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_005909.5:c.5368C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Periventricular nodular heterotopia 9
Identifiers:: MONDO: MONDO:0030061; MedGen: C5394503; OMIM: 618918

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003841955	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 23, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30979967, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003841955

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 23, 2023)

unknown

clinical testing

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Unique bioinformatic approach and comprehensive reanalysis improve diagnostic yield of clinical exomes.

Schmitz-Abe K, Li Q, Rosen SM, Nori N, Madden JA, Genetti CA, Wojcik MH, Ponnaluri S, Gubbels CS, Picker JD, O'Donnell-Luria AH, Yu TW, Bodamer O, Brownstein CA, Beggs AH, Agrawal PB.

Eur J Hum Genet. 2019 Sep;27(9):1398-1405. doi: 10.1038/s41431-019-0401-x. Epub 2019 Apr 12.

PubMed [citation]

PMID:: 30979967
PMCID:: PMC6777619

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

Details of each submission

From 3billion, SCV003841955.1

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

Description

The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to be associated with MAP1B related disorder (ClinVar ID: VCV000638688 / PMID: 30979967). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Oct 8, 2024

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Relating variation to medicine