NM_006412.4(AGPAT2):c.685G>T (p.Glu229Ter) AND Congenital generalized lipodystrophy type 1

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Oct 20, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001706773.2

Allele description [Variation Report for NM_006412.4(AGPAT2):c.685G>T (p.Glu229Ter)]

NM_006412.4(AGPAT2):c.685G>T (p.Glu229Ter)

Gene:

AGPAT2:1-acylglycerol-3-phosphate O-acyltransferase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_006412.4(AGPAT2):c.685G>T (p.Glu229Ter)

HGVS:

NC_000009.12:g.136673904C>A
NG_008090.1:g.18556G>T
NM_001012727.2:c.589G>T
NM_006412.4:c.685G>TMANE SELECT
NP_001012745.1:p.Glu197Ter
NP_006403.2:p.Glu229Ter
NC_000009.11:g.139568356C>A

Protein change:

E197*; GLU229TER

Links:

OMIM: 603100.0010; dbSNP: rs1255380257

NCBI 1000 Genomes Browser:

rs1255380257

Molecular consequence:

NM_001012727.2:c.589G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_006412.4:c.685G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Congenital generalized lipodystrophy type 1 (CGL1)
Synonyms:: BRUNZELL SYNDROME, AGPAT2-RELATED
Identifiers:: MONDO: MONDO:0012071; MedGen: C1720862; Orphanet: 528; OMIM: 608594

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001934254	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 20, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003935985	OMIM	no assertion criteria provided	Pathogenic (Jun 27, 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

SCV001934254

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 20, 2020)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003935985

OMIM

no assertion criteria provided

Pathogenic
(Jun 27, 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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Congenital generalized lipodystrophy: The evaluation of clinical follow-up findings in a series of five patients with type 1 and two patients with type 4.

Nilay Güneş, Kutlu T, Tekant GT, Eroğlu AG, Üstündağ NÇ, Öztürk B, Onay H, Tüysüz B.

Eur J Med Genet. 2020 Apr;63(4):103819. doi: 10.1016/j.ejmg.2019.103819. Epub 2019 Nov 25.

PubMed [citation]

PMID:: 31778856

Details of each submission

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001934254.1

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

Description

This variant was identified as homozygous.

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

From OMIM, SCV003935985.1

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

Description

In a patient, born of consanguineous Turkish parents (family 3), with congenital lipodystrophy-1 (CGL1; 608594), Gunes et al. (2020) identified homozygosity for a c.685G-T transversion in the AGPAT2 gene, resulting in a glu229-to-ter (E229X) substitution. The mutation was identified by whole-exome sequencing of 4 genes associated with lipodystrophy. Functional studies were not performed.

#	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: Dec 24, 2023

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