5-150056097-A-G

Variant names:

• chr5-150056097-A-G
• rs397515557
• NM_001288705.3:c.2483T>C

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 9P and 0B. PM1 PM2 PP3_Strong PP5

The NM_001288705.3(CSF1R):​c.2483T>C​(p.Phe828Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: CSF1R NM_001288705.3 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 9.31
• Publications: 5 publications found

Genes affected

CSF1R (HGNC:2433): (colony stimulating factor 1 receptor) The protein encoded by this gene is the receptor for colony stimulating factor 1, a cytokine which controls the production, differentiation, and function of macrophages. This receptor mediates most if not all of the biological effects of this cytokine. Ligand binding activates the receptor kinase through a process of oligomerization and transphosphorylation. The encoded protein is a tyrosine kinase transmembrane receptor and member of the CSF1/PDGF receptor family of tyrosine-protein kinases. Mutations in this gene have been associated with a predisposition to myeloid malignancy. The first intron of this gene contains a transcriptionally inactive ribosomal protein L7 processed pseudogene oriented in the opposite direction. Alternative splicing results in multiple transcript variants. Expression of a splice variant from an LTR promoter has been found in Hodgkin lymphoma (HL), HL cell lines and anaplastic large cell lymphoma. [provided by RefSeq, Mar 2017]

CSF1R Gene-Disease associations (from GenCC):

• hereditary diffuse leukoencephalopathy with axonal spheroids and pigmented glia

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Genomics England PanelApp, Orphanet
• brain abnormalities, neurodegeneration, and dysosteosclerosis

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
• leukoencephalopathy, diffuse hereditary, with spheroids 1

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• early-onset calcifying leukoencephalopathy-skeletal dysplasia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_pathogenic. The variant received 9 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 5 uncertain in NM_001288705.3
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.973
• PP5: Variant 5-150056097-A-G is Pathogenic according to our data. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-150056097-A-G is described in CliVar as Pathogenic. Clinvar id is 65686.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSF1R	NM_001288705.3	c.2483T>C	p.Phe828Ser	missense_variant	Exon 18 of 21	ENST00000675795.1	NP_001275634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSF1R	ENST00000675795.1	c.2483T>C	p.Phe828Ser	missense_variant	Exon 18 of 21		NM_001288705.3	ENSP00000501699.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Hereditary diffuse leukoencephalopathy with spheroids Pathogenic:1

Aug 30, 2012

GeneReviews

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: curation

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.070
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.67	D
Eigen	Uncertain	0.45
Eigen_PC	Uncertain	0.51
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.93	D
M_CAP	Pathogenic	0.66	D
MetaRNN	Pathogenic	0.97	D
MetaSVM	Uncertain	0.12	D
MutationAssessor	Benign	0.25	N
PhyloP100		9.3
PrimateAI	Pathogenic	0.87	D
PROVEAN	Pathogenic	-6.5	D
REVEL	Pathogenic	0.75
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0060	D
Polyphen		1.0	D
Vest4		0.94
MutPred		0.78		Loss of stability (P = 0.008);
MVP		0.93
MPC		4.3
ClinPred		1.0	D
GERP RS		4.7
Varity_R		0.95
gMVP		0.96
Mutation Taster		=9/91	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs397515557; hg19: chr5-149435660;