NM_004736.4(XPR1):c.419T>C (p.Leu140Pro) AND Basal ganglia calcification, idiopathic, 6

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 1, 2015
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:: RCV000172881.2

Allele description [Variation Report for NM_004736.4(XPR1):c.419T>C (p.Leu140Pro)]

NM_004736.4(XPR1):c.419T>C (p.Leu140Pro)

Gene:

XPR1:xenotropic and polytropic retrovirus receptor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q25.3

Genomic location:

Preferred name:

NM_004736.4(XPR1):c.419T>C (p.Leu140Pro)

HGVS:

NC_000001.11:g.180803583T>C
NG_050964.1:g.176574T>C
NM_001135669.2:c.419T>C
NM_001328662.2:c.419T>C
NM_004736.4:c.419T>CMANE SELECT
NP_001129141.1:p.Leu140Pro
NP_001315591.1:p.Leu140Pro
NP_004727.2:p.Leu140Pro
NC_000001.10:g.180772719T>C
NM_004736.3:c.419T>C
NR_137330.2:n.599T>C
Q9UBH6:p.Leu140Pro

Protein change:

L140P; LEU140PRO

Links:

UniProtKB: Q9UBH6#VAR_073841; OMIM: 605237.0003; dbSNP: rs786205903

NCBI 1000 Genomes Browser:

rs786205903

Molecular consequence:

NM_001135669.2:c.419T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001328662.2:c.419T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004736.4:c.419T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_137330.2:n.599T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Basal ganglia calcification, idiopathic, 6 (IBGC6)
Identifiers:: MONDO: MONDO:0014628; MedGen: C4225335; Orphanet: 1980; OMIM: 616413

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000223871	OMIM	no assertion criteria provided	Pathogenic (Jun 1, 2015)	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

SCV000223871

OMIM

no assertion criteria provided

Pathogenic
(Jun 1, 2015)

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

Mutations in XPR1 cause primary familial brain calcification associated with altered phosphate export.

Legati A, Giovannini D, Nicolas G, López-Sánchez U, Quintáns B, Oliveira JR, Sears RL, Ramos EM, Spiteri E, Sobrido MJ, Carracedo Á, Castro-Fernández C, Cubizolle S, Fogel BL, Goizet C, Jen JC, Kirdlarp S, Lang AE, Miedzybrodzka Z, Mitarnun W, Paucar M, Paulson H, et al.

Nat Genet. 2015 Jun;47(6):579-81. doi: 10.1038/ng.3289. Epub 2015 May 4.

PubMed [citation]

PMID:: 25938945
PMCID:: PMC4516721

Details of each submission

From OMIM, SCV000223871.1

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

Description

In a man with idiopathic basal ganglia calcification-6 (IBGC6; 616413), Legati et al. (2015) identified a heterozygous c.419T-C transition (c.419T-C, NM_004736.3) in the XPR1 gene, resulting in a leu140-to-pro (L140P) substitution at a conserved residue in the SPX domain. The mutation was not found in the dbSNP (build 138), 1000 Genomes Project, Exome Variant Server, or Exome Aggregation Consortium databases, or in 287 in-house control exomes. In vitro studies showed that the mutant protein was present at the plasma membrane and served as a retroviral receptor, but phosphate efflux was impaired.

#	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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