NM_173582.6(PGM2L1):c.1115del (p.Asn372fs) AND Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 11, 2023
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV003225748.1

Allele description [Variation Report for NM_173582.6(PGM2L1):c.1115del (p.Asn372fs)]

NM_173582.6(PGM2L1):c.1115del (p.Asn372fs)

Gene:

PGM2L1:phosphoglucomutase 2 like 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q13.4

Genomic location:

Preferred name:

NM_173582.6(PGM2L1):c.1115del (p.Asn372fs)

HGVS:

NC_000011.10:g.74345576del
NC_000011.9:g.74056617del
NM_173582.6:c.1115delMANE SELECT
NP_775853.2:p.Asn372fs
NC_000011.9:g.74056617del
NC_000011.9:g.74056617delT
NC_000011.9:g.74056621del

Protein change:

N372fs

Links:

OMIM: 611610.0003; dbSNP: rs2134888290

NCBI 1000 Genomes Browser:

rs2134888290

Molecular consequence:

NM_173582.6:c.1115del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities (NEDHFS)
Identifiers:: MONDO: MONDO:0859347; MedGen: C5774285; OMIM: 620191

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003840952	OMIM	no assertion criteria provided	Pathogenic (Jan 11, 2023)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003840952

OMIM

no assertion criteria provided

Pathogenic
(Jan 11, 2023)

germline

literature only

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	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Impaired glucose-1,6-biphosphate production due to bi-allelic PGM2L1 mutations is associated with a neurodevelopmental disorder.

Morava E, Schatz UA, Torring PM, Abbott MA, Baumann M, Brasch-Andersen C, Chevalier N, Dunkhase-Heinl U, Fleger M, Haack TB, Nelson S, Potelle S, Radenkovic S, Bommer GT, Van Schaftingen E, Veiga-da-Cunha M.

Am J Hum Genet. 2021 Jun 3;108(6):1151-1160. doi: 10.1016/j.ajhg.2021.04.017. Epub 2021 May 11.

PubMed [citation]

PMID:: 33979636
PMCID:: PMC8206387

Details of each submission

From OMIM, SCV003840952.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

For discussion of the 1-bp deletion in the PGM2L1 gene (c.1115delA, NM_173582), resulting in a frameshift and premature termination (Asn372IlefsTer8), that was found in compound heterozygous state in a patient with neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities (NEDHFS; 620191) by Morava et al. (2021), see 611610.0002.

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

Last Updated: Sep 29, 2024

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