NM_000290.4(PGAM2):c.233G>A (p.Trp78Ter) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jan 6, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000493394.12

Allele description [Variation Report for NM_000290.4(PGAM2):c.233G>A (p.Trp78Ter)]

NM_000290.4(PGAM2):c.233G>A (p.Trp78Ter)

Genes:

LOC129998343:ATAC-STARR-seq lymphoblastoid active region 25926 [Gene]
DBNL:drebrin like [Gene - OMIM - HGNC]
PGAM2:phosphoglycerate mutase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p13

Genomic location:

Preferred name:

NM_000290.4(PGAM2):c.233G>A (p.Trp78Ter)

HGVS:

NC_000007.14:g.44065297C>T
NG_013016.1:g.5291G>A
NM_000290.4:c.233G>AMANE SELECT
NM_001014436.3:c.*4381C>TMANE SELECT
NM_001122956.2:c.*4381C>T
NM_001284313.2:c.*4381C>T
NM_001362723.2:c.*4381C>T
NM_014063.7:c.*4381C>T
NP_000281.2:p.Trp78Ter
NC_000007.13:g.44104896C>T
NM_000290.3:c.233G>A
p.Trp78*

Protein change:

W78*; TRP78TER

Links:

OMIM: 612931.0001; dbSNP: rs10250779

NCBI 1000 Genomes Browser:

rs10250779

Molecular consequence:

NM_001014436.3:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001122956.2:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001284313.2:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001362723.2:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_014063.7:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000290.4:c.233G>A - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Arachis hypogaea DNA, clone: KIAC14G22, genomic survey sequence
Arachis hypogaea DNA, clone: KIAC14G22, genomic survey sequence
gi|387519329|dbj|DH965046.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000224186	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Dec 29, 2014)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23169535, 8447317 Citation Link,
SCV000582131	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jan 6, 2022)	germline	clinical testing	Citation Link,
SCV000801666	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 4, 2020)	germline	clinical testing	PubMed (12) [See all records that cite these PMIDs] 8447317, 27612597, 23169535, 19783439, 16881065, 10545043, 18852891, 26502762, 28944235, 21444020, 23335027, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000224186

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Dec 29, 2014)

germline

clinical testing

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

Citation Link,

SCV000582131

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jan 6, 2022)

germline

clinical testing

Citation Link,

SCV000801666

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 4, 2020)

germline

clinical testing

PubMed (12)
[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	germline	unknown	6	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The molecular genetic basis of muscle phosphoglycerate mutase (PGAM) deficiency.

Tsujino S, Shanske S, Sakoda S, Fenichel G, DiMauro S.

Am J Hum Genet. 1993 Mar;52(3):472-7.

PubMed [citation]

PMID:: 8447317
PMCID:: PMC1682163

Phosphoglycerate mutase deficiency (glycogen storage disease X) caused by a novel variant in PGAM-M.

Koo B, Oskarsson B.

Neuromuscul Disord. 2016 Oct;26(10):688-690. doi: 10.1016/j.nmd.2016.08.002. Epub 2016 Aug 11.

PubMed [citation]

PMID:: 27612597

See all PubMed Citations (12)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000224186.5

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

#	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		4	not provided	not provided	not provided

From GeneDx, SCV000582131.6

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

Description

The most common pathogenic variant identified in patients of African ancestry with PGAM deficiency, likely due to a founder effect (Koo et al., 2016); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 8447317, 23169535, 27612597, 28944235, 19783439, 28492532, 6308514, 2987758, 31589614, 27535533)

#	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

From Mayo Clinic Laboratories, Mayo Clinic, SCV000801666.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (12)

Description

PVS1, PS4, PP4

#	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		2	not provided	not provided	not provided

Last Updated: Mar 16, 2024

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