NM_018960.6(GNMT):c.149T>C (p.Leu50Pro) AND Glycine N-methyltransferase deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 1, 2002
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:: RCV000004386.3

Allele description [Variation Report for NM_018960.6(GNMT):c.149T>C (p.Leu50Pro)]

NM_018960.6(GNMT):c.149T>C (p.Leu50Pro)

Genes:

CNPY3-GNMT:CNPY3-GNMT readthrough [Gene]
GNMT:glycine N-methyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.1

Genomic location:

Preferred name:

NM_018960.6(GNMT):c.149T>C (p.Leu50Pro)

Other names:

L49P

HGVS:

NC_000006.12:g.42960916T>C
NG_008396.1:g.5155T>C
NG_108255.1:g.544T>C
NM_001318856.2:c.9-1296T>C
NM_001318857.2:c.152-1846T>C
NM_001318858.2:c.152-1846T>C
NM_001318865.2:c.149T>C
NM_018960.6:c.149T>CMANE SELECT
NP_001305794.1:p.Leu50Pro
NP_061833.1:p.Leu50Pro
NC_000006.11:g.42928654T>C
NR_134899.2:n.163T>C
Q14749:p.Leu50Pro

Protein change:

L50P; LEU49PRO

Links:

UniProtKB: Q14749#VAR_012766; OMIM: 606628.0001; dbSNP: rs121907888

NCBI 1000 Genomes Browser:

rs121907888

Molecular consequence:

NM_001318856.2:c.9-1296T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001318857.2:c.152-1846T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001318858.2:c.152-1846T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001318865.2:c.149T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_018960.6:c.149T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_134899.2:n.163T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Glycine N-methyltransferase deficiency
Identifiers:: MONDO: MONDO:0011698; MedGen: C1847720; OMIM: 606664

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000024558	OMIM	no assertion criteria provided	Pathogenic (Jan 1, 2002)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 11596649, 11810299

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000024558

OMIM

no assertion criteria provided

Pathogenic
(Jan 1, 2002)

germline

literature only

PubMed (2)
[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	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Glycine N-methyltransferase deficiency: a novel inborn error causing persistent isolated hypermethioninaemia.

Mudd SH, Cerone R, Schiaffino MC, Fantasia AR, Minniti G, Caruso U, Lorini R, Watkins D, Matiaszuk N, Rosenblatt DS, Schwahn B, Rozen R, LeGros L, Kotb M, Capdevila A, Luka Z, Finkelstein JD, Tangerman A, Stabler SP, Allen RH, Wagner C.

J Inherit Metab Dis. 2001 Aug;24(4):448-64.

PubMed [citation]

PMID:: 11596649

Mutations in human glycine N-methyltransferase give insights into its role in methionine metabolism.

Luka Z, Cerone R, Phillips JA 3rd, Mudd HS, Wagner C.

Hum Genet. 2002 Jan;110(1):68-74. Epub 2001 Dec 7.

PubMed [citation]

PMID:: 11810299

Details of each submission

From OMIM, SCV000024558.2

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

Description

In 2 Italian sibs with GNMT deficiency (606664) reported by Mudd et al. (2001), Luka et al. (2002) found compound heterozygosity for 2 missense mutations in the GNMT gene. One mutation was a 1481T-C transition in exon 1 resulting in a leu49-to-pro (L49P) substitution; the other was a 3715C-A transversion in exon 4 resulting in a his176-to-asn substitution (H176N; 606628.0002). The mother was heterozygous for the former mutation, and the father was heterozygous for the latter.

#	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 1, 2024

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