NM_001288705.3(CSF1R):c.2527_2530delinsGGCA (p.Ile843_Leu844delinsGlyIle) AND Hereditary diffuse leukoencephalopathy with spheroids

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 26, 2018
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:: RCV000754617.2

Allele description [Variation Report for NM_001288705.3(CSF1R):c.2527_2530delinsGGCA (p.Ile843_Leu844delinsGlyIle)]

NM_001288705.3(CSF1R):c.2527_2530delinsGGCA (p.Ile843_Leu844delinsGlyIle)

Gene:

CSF1R:colony stimulating factor 1 receptor [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

5q32

Genomic location:

Preferred name:

NM_001288705.3(CSF1R):c.2527_2530delinsGGCA (p.Ile843_Leu844delinsGlyIle)

HGVS:

NC_000005.10:g.150056050_150056053delinsTGCC
NG_012303.2:g.62320_62323delinsGGCA
NM_001288705.3:c.2527_2530delinsGGCAMANE SELECT
NM_001349736.2:c.2527_2530delinsGGCA
NM_001375320.1:c.2527_2530delinsGGCA
NM_001375321.1:c.2083_2086delinsGGCA
NM_005211.4:c.2527_2530delinsGGCA
NP_001275634.1:p.Ile843_Leu844delinsGlyIle
NP_001336665.1:p.Ile843_Leu844delinsGlyIle
NP_001362249.1:p.Ile843_Leu844delinsGlyIle
NP_001362250.1:p.Ile695_Leu696delinsGlyIle
NP_005202.2:p.Ile843_Leu844delinsGlyIle
NC_000005.9:g.149435613_149435616delinsTGCC
NR_109969.2:n.2491_2494delinsGGCA
NR_164679.1:n.2420_2423delinsGGCA

Links:

dbSNP: rs1561904557

NCBI 1000 Genomes Browser:

rs1561904557

Molecular consequence:

NM_001288705.3:c.2527_2530delinsGGCA - missense variant - [Sequence Ontology: SO:0001583]
NM_001349736.2:c.2527_2530delinsGGCA - missense variant - [Sequence Ontology: SO:0001583]
NM_001375320.1:c.2527_2530delinsGGCA - missense variant - [Sequence Ontology: SO:0001583]
NM_001375321.1:c.2083_2086delinsGGCA - missense variant - [Sequence Ontology: SO:0001583]
NM_005211.4:c.2527_2530delinsGGCA - missense variant - [Sequence Ontology: SO:0001583]
NR_109969.2:n.2491_2494delinsGGCA - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164679.1:n.2420_2423delinsGGCA - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Functional consequence:

Increased function

Observations:

Condition(s)

Name:: Hereditary diffuse leukoencephalopathy with spheroids
Synonyms:: LEUKOENCEPHALOPATHY, ADULT-ONSET, WITH AXONAL SPHEROIDS AND PIGMENTED GLIA
Identifiers:: MONDO: MONDO:0030796; MedGen: C3711381; Orphanet: 313808; OMIM: PS221820

Recent activity

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Gene neighbors for Gene (Select 338773) (7)
Gene
MAG: Acidobacteria bacterium UBA6911 isolate CB27_Tmax.123 genome assembly, cont...
MAG: Acidobacteria bacterium UBA6911 isolate CB27_Tmax.123 genome assembly, contig: Ga0310121_10000149, whole genome shotgun sequence
gi|2617705189|emb|CAUZIZ010000005.1 |WGS:CAUZIZ01|Ga0310121_10000149

Nucleotide
Concise Conserved Domain Links for Protein (Select 18266781) (1)
Conserved Domains
Human DNA sequence from clone RP11-296H2 on chromosome 10, complete sequence
Human DNA sequence from clone RP11-296H2 on chromosome 10, complete sequence
gi|14800005|emb|AL135793.13|

Nucleotide
txid2724165[Organism:noexp] (2)
BioProject

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000787829	Institute of Human Genetics, Martin Luther University Halle-Wittenberg	no assertion criteria provided	Pathogenic (Jul 26, 2018)	unknown, not applicable	clinical testing, in vivo

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000787829

Institute of Human Genetics, Martin Luther University Halle-Wittenberg

no assertion criteria provided

Pathogenic
(Jul 26, 2018)

unknown, not applicable

clinical testing, in vivo

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	not applicable	not applicable	not provided	not provided	not provided	not provided	not provided	in vivo
Caucasian	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Institute of Human Genetics, Martin Luther University Halle-Wittenberg, SCV000787829.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	in vivo	not provided
2	Caucasian	1	not provided	not provided	clinical testing	not provided

Description

By flow cytometric analysis of peripheral blood monocytes, slightly elevated cell surface levels of CSF1R and increased autophosphorylation were observed.

Description

The heterozygous variant NM_005211.3(CSF1R):c.2527_2530delinsGGCA (p.Ile843_Leu844delinsGlyIle) affects the same codon as known pathogenic variants NM_005211.3(CSF1R):c.2527A>T (p.Ile843Phe) and NM_005211.3(CSF1R):c.2528T>A (p.Ile843Asn). Furthermore there is functional and clear clinical evidence that above mentioned variant meets our criteria to be classified as pathogenic.

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

Last Updated: Mar 30, 2024

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