NM_000430.4(PAFAH1B1):c.703_704del (p.Glu235fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 22, 2018
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:: RCV000599007.2

Allele description [Variation Report for NM_000430.4(PAFAH1B1):c.703_704del (p.Glu235fs)]

NM_000430.4(PAFAH1B1):c.703_704del (p.Glu235fs)

Gene:

PAFAH1B1:platelet activating factor acetylhydrolase 1b regulatory subunit 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

17p13.3

Genomic location:

Preferred name:

NM_000430.4(PAFAH1B1):c.703_704del (p.Glu235fs)

HGVS:

NC_000017.11:g.2674089GA[1]
NG_009799.1:g.85461GA[1]
NM_000430.4:c.703_704delMANE SELECT
NP_000421.1:p.Glu235fs
NC_000017.10:g.2577383GA[1]
NM_000430.3:c.703_704del
NM_000430.3:c.703_704delGA

Protein change:

E235fs

Links:

dbSNP: rs797045865

NCBI 1000 Genomes Browser:

rs797045865

Molecular consequence:

NM_000430.4:c.703_704del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000709919	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Feb 22, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000709919

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Feb 22, 2018)

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

Details of each submission

From GeneDx, SCV000709919.2

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

Description

The c.703_704delGA pathogenic variant in the PAFAH1B1 gene has been reported previously as a denovo variant in an individual with isolated lissencephaly sequence (ILS) (Pilz et al., 1998). Thedeletion causes a frameshift starting with codon Glutamic acid 235, changes this amino acid to aMethionine residue and creates a premature Stop codon at position 20 of the new reading frame,denoted p.Glu235MetfsX20. This pathogenic variant is predicted to cause loss of normal proteinfunction either through protein truncation or nonsense-mediated mRNA decay. Furthermore, thec.703_704delGA variant is not observed in large population cohorts (Lek et al., 2016). The presence of this pathogenic variant is consistent with the diagnosis of a PAFAH1B1-related disorder in this individual.

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

Last Updated: Mar 16, 2024

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