chr3-46357586-T-TAC
Position:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_001123396.4(CCR2):c.59_60insAC(p.Thr21ProfsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
CCR2
NM_001123396.4 frameshift
NM_001123396.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.10
Genes affected
CCR2 (HGNC:1603): (C-C motif chemokine receptor 2) The protein encoded by this gene is a receptor for monocyte chemoattractant protein-1, a chemokine which specifically mediates monocyte chemotaxis. Monocyte chemoattractant protein-1 is involved in monocyte infiltration in inflammatory diseases such as rheumatoid arthritis as well as in the inflammatory response against tumors. The encoded protein mediates agonist-dependent calcium mobilization and inhibition of adenylyl cyclase. This protein can also be a coreceptor with CD4 for HIV-1 infection. This gene is located in the chemokine receptor gene cluster region of chromosome 3. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 5 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-46357586-T-TAC is Pathogenic according to our data. Variant chr3-46357586-T-TAC is described in ClinVar as [Pathogenic]. Clinvar id is 3061928.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCR2 | NM_001123396.4 | c.59_60insAC | p.Thr21ProfsTer18 | frameshift_variant | 2/2 | ENST00000445132.3 | |
CCR2 | NM_001123041.3 | c.59_60insAC | p.Thr21ProfsTer18 | frameshift_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCR2 | ENST00000445132.3 | c.59_60insAC | p.Thr21ProfsTer18 | frameshift_variant | 2/2 | 1 | NM_001123396.4 | P2 | |
CCR2 | ENST00000400888.2 | c.59_60insAC | p.Thr21ProfsTer18 | frameshift_variant | 1/2 | 1 | A2 | ||
CCR2 | ENST00000421659.1 | c.59_60insAC | p.Thr21ProfsTer18 | frameshift_variant | 3/3 | 4 | |||
CCR2 | ENST00000465202.1 | n.315-531_315-530insAC | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Bravo
AF:
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Cystic disease of lung Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 12, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at