17-74367706-C-G

Variant names:

• chr17-74367706-C-G
• ENST00000335666.4:c.201C>G
• GPR142 p.Asp67Glu

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_181790.1(GPR142):​c.201C>G​(p.Asp67Glu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GPR142 NM_181790.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.42
• Publications: 0 publications found

Genes affected

GPR142 (HGNC:20088): (G protein-coupled receptor 142) GPR142 is a member of the rhodopsin family of G protein-coupled receptors (GPRs) (Fredriksson et al., 2003 [PubMed 14623098]).[supplied by OMIM, Mar 2008]

ACMG classification

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=0.10174844).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181790.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR142	NM_001331076.1	MANE Select	c.-162C>G		5_prime_UTR	Exon 1 of 4	NP_001318005.1	Q7Z601
	GPR142	NM_181790.1		c.201C>G	p.Asp67Glu	missense	Exon 1 of 4	NP_861455.1	Q7Z601
	GPR142	NM_001331077.1		c.-116C>G		5_prime_UTR	Exon 1 of 4	NP_001318006.1	Q7Z601

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR142	ENST00000335666.4	TSL:1	c.201C>G	p.Asp67Glu	missense	Exon 1 of 4	ENSP00000335158.4	Q7Z601
	GPR142	ENST00000582579.6	TSL:1 MANE Select	c.-162C>G		5_prime_UTR	Exon 1 of 4	ENSP00000464632.2	J3QSD0
	GPR142	ENST00000585308.6	TSL:3	c.-116C>G		5_prime_UTR	Exon 1 of 4	ENSP00000463521.2	J3QLF2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	13
DANN	Uncertain	0.98
DEOGEN2	Benign	0.0043	T
Eigen	Benign	-0.86
Eigen_PC	Benign	-0.85
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.34	T
M_CAP	Benign	0.0059	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	0.0	N
PhyloP100		4.4
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-0.38	N
REVEL	Benign	0.24
Sift	Pathogenic	0.0	D
PromoterAI		-0.015	Neutral
Varity_R		0.071
gMVP		0.021

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-72363845;