NM_001375808.2(LPIN2):c.1673G>A (p.Trp558Ter) AND Majeed syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 13, 2023
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:: RCV003504975.1

Allele description [Variation Report for NM_001375808.2(LPIN2):c.1673G>A (p.Trp558Ter)]

NM_001375808.2(LPIN2):c.1673G>A (p.Trp558Ter)

Gene:

LPIN2:lipin 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18p11.31

Genomic location:

Preferred name:

NM_001375808.2(LPIN2):c.1673G>A (p.Trp558Ter)

HGVS:

NC_000018.10:g.2927759C>T
NG_007507.1:g.89189G>A
NM_001375808.2:c.1673G>AMANE SELECT
NM_001375809.1:c.1673G>A
NM_014646.2:c.1673G>A
NP_001362737.1:p.Trp558Ter
NP_001362738.1:p.Trp558Ter
NP_055461.1:p.Trp558Ter
LRG_174t1:c.1673G>A
LRG_174:g.89189G>A
LRG_174p1:p.Trp558Ter
NC_000018.9:g.2927757C>T

Protein change:

W558*

Molecular consequence:

NM_001375808.2:c.1673G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001375809.1:c.1673G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_014646.2:c.1673G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Majeed syndrome (MJDS)
Synonyms:: Chronic recurrent multifocal osteomyelitis, congenital; Dyserythropoietic anemia, and neutrophilic dermatosis; Congenital dyserythropoietic anemia and chronic recurrent multifocal osteomyelitis; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012316; MedGen: C1864997; Orphanet: 77297; OMIM: 609628

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004328222	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 13, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15994876, 23087183, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004328222

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 13, 2023)

germline

clinical testing

PubMed (3)
[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	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Homozygous mutations in LPIN2 are responsible for the syndrome of chronic recurrent multifocal osteomyelitis and congenital dyserythropoietic anaemia (Majeed syndrome).

Ferguson PJ, Chen S, Tayeh MK, Ochoa L, Leal SM, Pelet A, Munnich A, Lyonnet S, Majeed HA, El-Shanti H.

J Med Genet. 2005 Jul;42(7):551-7.

PubMed [citation]

PMID:: 15994876
PMCID:: PMC1736104

Efficacy of anti-IL-1 treatment in Majeed syndrome.

Herlin T, Fiirgaard B, Bjerre M, Kerndrup G, Hasle H, Bing X, Ferguson PJ.

Ann Rheum Dis. 2013 Mar;72(3):410-3. doi: 10.1136/annrheumdis-2012-201818. Epub 2012 Oct 20.

PubMed [citation]

PMID:: 23087183
PMCID:: PMC3660147

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004328222.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Trp558*) in the LPIN2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LPIN2 are known to be pathogenic (PMID: 15994876, 23087183). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LPIN2-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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