NM_145262.4(GLYCTK):c.1448del (p.Phe483fs) AND D-Glyceric aciduria

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Dec 1, 2010
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:: RCV000077847.3

Allele description [Variation Report for NM_145262.4(GLYCTK):c.1448del (p.Phe483fs)]

NM_145262.4(GLYCTK):c.1448del (p.Phe483fs)

Gene:

GLYCTK:glycerate kinase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p21.2

Genomic location:

Preferred name:

NM_145262.4(GLYCTK):c.1448del (p.Phe483fs)

HGVS:

NC_000003.12:g.52293002del
NG_023246.1:g.10183del
NM_001144951.2:c.*567del
NM_145262.4:c.1448delMANE SELECT
NP_660305.2:p.Phe483fs
NC_000003.11:g.52327018del
NM_145262.3:c.1448delT
NR_026699.2:n.1538del
NR_026701.2:n.1536del

Protein change:

F483fs

Links:

OMIM: 610516.0001; dbSNP: rs121909447

NCBI 1000 Genomes Browser:

rs121909447

Molecular consequence:

NM_001144951.2:c.*567del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_145262.4:c.1448del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_026699.2:n.1538del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_026701.2:n.1536del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: D-Glyceric aciduria
Synonyms:: GLYCERATE KINASE DEFICIENCY; D-Glycerate kinase deficiency; Non ketotic hyperglycinemia syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009070; MedGen: C0342765; Orphanet: 941; OMIM: 220120

Recent activity

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LOC108337214 [Vigna angularis]
LOC108337214 [Vigna angularis]
Gene ID:108337214

Gene
FOMMEDRAFT_111729 [Fomitiporia mediterranea MF3/22]
FOMMEDRAFT_111729 [Fomitiporia mediterranea MF3/22]
Gene ID:18670607

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000045111	OMIM	no assertion criteria provided	Pathogenic (Dec 1, 2010)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 4434100, 20949620
SCV000109693	Universitäts-Kinderspital Zürich	no classification provided	not provided	unknown	not provided

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000045111

OMIM

no assertion criteria provided

Pathogenic
(Dec 1, 2010)

germline

literature only

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

SCV000109693

Universitäts-Kinderspital Zürich

no classification provided

not provided

unknown

not provided

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	not provided	not provided	not provided	not provided	not provided	2	not provided	literature only
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Letter: Hyperglycericacidaemia with hyperglycinaemia: a new inborn error of metabolism.

Brandt NJ, Brandt S, Rasmussen K, Schnoheyder F.

Br Med J. 1974 Nov 9;4(5940):344. No abstract available.

PubMed [citation]

PMID:: 4434100
PMCID:: PMC1612942

D-glyceric aciduria is caused by genetic deficiency of D-glycerate kinase (GLYCTK).

Sass JO, Fischer K, Wang R, Christensen E, Scholl-Bürgi S, Chang R, Kapelari K, Walter M.

Hum Mutat. 2010 Dec;31(12):1280-5. doi: 10.1002/humu.21375. Epub 2010 Nov 9.

PubMed [citation]

PMID:: 20949620

Details of each submission

From OMIM, SCV000045111.3

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

Description

In fibroblasts taken from a Serbian boy with D-glyceric aciduria (220120), originally reported by Brandt et al. (1974), Sass et al. (2010) identified a homozygous 1-bp deletion (1448delT) in exon 5 of the GLYCTK gene, resulting in a frameshift and premature termination. In vitro functional expression studies in HEK293 cells showed that the mutant protein was not expressed and had no enzymatic activity. The mutation was not found in 214 control chromosomes. Clinical features reported by Brandt et al. (1974) included neonatal hypotonia, delayed psychomotor development, mental retardation, and seizures.

Increased glycine in the patient studied by Brandt et al. (1974) and Sass et al. (2010) was found to be the result of homozygous mutation in the AMT gene (238310.0009); thus, 2 rare inborn errors of metabolism, D-glyceric aciduria and glycine encephalopathy (605899), coexisted in this patient.

#	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

From Universitäts-Kinderspital Zürich, SCV000109693.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	not provided	2	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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