NM_006623.4(PHGDH):c.138+2dup AND PHGDH deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 5, 2020
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:: RCV001172238.2

Allele description [Variation Report for NM_006623.4(PHGDH):c.138+2dup]

NM_006623.4(PHGDH):c.138+2dup

Gene:

PHGDH:phosphoglycerate dehydrogenase [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

1p12

Genomic location:

Preferred name:

NM_006623.4(PHGDH):c.138+2dup

HGVS:

NC_000001.11:g.119712162dup
NG_009188.1:g.5367dup
NM_006623.4:c.138+2dupMANE SELECT
NC_000001.10:g.120254785dup
NM_006623.3:c.138+2dupT
c.138+2dupT

Links:

OMIM: 606879.0012; dbSNP: rs1650723432

NCBI 1000 Genomes Browser:

rs1650723432

Molecular consequence:

NM_006623.4:c.138+2dup - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: PHGDH deficiency
Synonyms:: Phosphoglycerate dehydrogenase deficiency
Identifiers:: MONDO: MONDO:0011152; MedGen: C1866174; OMIM: 601815

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001335234	OMIM	no assertion criteria provided	Pathogenic (Jun 5, 2020)	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

SCV001335234

OMIM

no assertion criteria provided

Pathogenic
(Jun 5, 2020)

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

Infantile Serine Biosynthesis Defect Due to Phosphoglycerate Dehydrogenase Deficiency: Variability in Phenotype and Treatment Response, Novel Mutations, and Diagnostic Challenges.

Benke PJ, Hidalgo RJ, Braffman BH, Jans J, Gassen KLIV, Sunbul R, El-Hattab AW.

J Child Neurol. 2017 May;32(6):543-549. doi: 10.1177/0883073817690094. Epub 2017 Jan 31.

PubMed [citation]

PMID:: 28135894

Details of each submission

From OMIM, SCV001335234.1

#	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 duplication (c.138+2dupT, NM_006623.3) in the PHGDH gene that was found in compound heterozygous state in 2 sisters (family 1) with phosphoglycerate dehydrogenase deficiency (PHGDHD; 601815) by Benke et al. (2017), see 606879.0005.

#	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: Apr 23, 2022

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