GeneBe

rs1891005900

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001142343.2(CMKLR1):​c.595G>C​(p.Gly199Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G199E) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

CMKLR1
NM_001142343.2 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.02

Publications

0 publications found
Variant links:
Genes affected
CMKLR1 (HGNC:2121): (chemerin chemokine-like receptor 1) Enables adipokinetic hormone binding activity and adipokinetic hormone receptor activity. Involved in several processes, including negative regulation of NF-kappaB transcription factor activity; positive regulation of macrophage chemotaxis; and regulation of calcium-mediated signaling. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.073290825).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142343.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CMKLR1
NM_001142343.2
MANE Select
c.595G>Cp.Gly199Arg
missense
Exon 4 of 4NP_001135815.1Q99788-1
CMKLR1
NM_001142344.2
c.595G>Cp.Gly199Arg
missense
Exon 3 of 3NP_001135816.1Q99788-1
CMKLR1
NM_001142345.2
c.595G>Cp.Gly199Arg
missense
Exon 3 of 3NP_001135817.1Q99788-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CMKLR1
ENST00000550402.6
TSL:1 MANE Select
c.595G>Cp.Gly199Arg
missense
Exon 4 of 4ENSP00000449716.1Q99788-1
CMKLR1
ENST00000552995.5
TSL:1
c.589G>Cp.Gly197Arg
missense
Exon 3 of 3ENSP00000447579.1Q99788-2
CMKLR1
ENST00000312143.11
TSL:2
c.595G>Cp.Gly199Arg
missense
Exon 3 of 3ENSP00000311733.7Q99788-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
0.031
DANN
Benign
0.47
DEOGEN2
Benign
0.045
T
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.057
N
LIST_S2
Benign
0.50
T
M_CAP
Benign
0.0037
T
MetaRNN
Benign
0.073
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.78
N
PhyloP100
-2.0
PrimateAI
Benign
0.22
T
PROVEAN
Benign
0.010
N
REVEL
Benign
0.015
Sift
Benign
0.35
T
Sift4G
Benign
0.36
T
Polyphen
0.0010
B
Vest4
0.11
MutPred
0.51
Gain of catalytic residue at G199 (P = 0.002)
MVP
0.12
MPC
0.19
ClinPred
0.11
T
GERP RS
-6.1
Varity_R
0.031
gMVP
0.30
Mutation Taster
=93/7
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs1891005900; hg19: chr12-108686145; API