rs387906662
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_001288705.3(CSF1R):c.2509G>T(p.Asp837Tyr) 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. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. D837D) has been classified as Likely benign.
Frequency
Consequence
NM_001288705.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF1R | NM_001288705.3 | c.2509G>T | p.Asp837Tyr | missense_variant | 18/21 | ENST00000675795.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF1R | ENST00000675795.1 | c.2509G>T | p.Asp837Tyr | missense_variant | 18/21 | NM_001288705.3 | P1 | ||
CSF1R | ENST00000286301.7 | c.2509G>T | p.Asp837Tyr | missense_variant | 19/22 | 1 | P1 | ||
CSF1R | ENST00000504875.5 | c.*330G>T | 3_prime_UTR_variant, NMD_transcript_variant | 17/20 | 1 | ||||
CSF1R | ENST00000515068.1 | c.*483G>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Hereditary diffuse leukoencephalopathy with spheroids Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 25, 2011 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at