chr1-202951039-TG-T

Variant names:

• chr1-202951039-TG-T
• rs886039240
• NM_015999.6:c.31delC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_015999.6(ADIPOR1):​c.31delC​(p.Gln11ArgfsTer24) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ADIPOR1 NM_015999.6 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:2
• Conservation: PhyloP100: 4.21

Genes affected

ADIPOR1 (HGNC:24040): (adiponectin receptor 1) This gene encodes a protein which acts as a receptor for adiponectin, a hormone secreted by adipocytes which regulates fatty acid catabolism and glucose levels. Binding of adiponectin to the encoded protein results in activation of an AMP-activated kinase signaling pathway which affects levels of fatty acid oxidation and insulin sensitivity. A pseudogene of this gene is located on chromosome 14. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR1	NM_015999.6	c.31delC	p.Gln11ArgfsTer24	frameshift_variant	Exon 2 of 8	ENST00000340990.10	NP_057083.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR1	ENST00000340990.10	c.31delC	p.Gln11ArgfsTer24	frameshift_variant	Exon 2 of 8	1	NM_015999.6	ENSP00000341785.5
ADIPOR1	ENST00000367254.7	c.31delC	p.Gln11ArgfsTer24	frameshift_variant	Exon 2 of 7	1		ENSP00000356223.3
ADIPOR1	ENST00000417068.5	c.31delC	p.Gln11ArgfsTer24	frameshift_variant	Exon 3 of 7	3		ENSP00000402178.1
ADIPOR1	ENST00000426229.1	c.31delC	p.Gln11ArgfsTer24	frameshift_variant	Exon 3 of 6	2		ENSP00000392946.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:2

Jan 06, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ClinVar contains an entry for this variant (Variation ID: 264709). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This premature translational stop signal has been observed in individual(s) with autosomal recessive syndromic retinitis pigmentosa (PMID: 26662040). This sequence change creates a premature translational stop signal (p.Gln11Argfs*24) in the ADIPOR1 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in ADIPOR1 cause disease. This variant is not present in population databases (gnomAD no frequency). -

Oct 03, 2016

OMIM

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs886039240; hg19: chr1-202920167;