20-58910818-G-T

Position:

• chr20-58910818-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_Moderate PM2 PP5

The NM_000516.7(GNAS):​c.1174G>T​(p.Glu392*) variant causes a stop gained 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. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: GNAS NM_000516.7 stop_gained
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 9.52

Genes affected

GNAS (HGNC:4392): (GNAS complex locus) This locus has a highly complex imprinted expression pattern. It gives rise to maternally, paternally, and biallelically expressed transcripts that are derived from four alternative promoters and 5' exons. Some transcripts contain a differentially methylated region (DMR) at their 5' exons, and this DMR is commonly found in imprinted genes and correlates with transcript expression. An antisense transcript is produced from an overlapping locus on the opposite strand. One of the transcripts produced from this locus, and the antisense transcript, are paternally expressed noncoding RNAs, and may regulate imprinting in this region. In addition, one of the transcripts contains a second overlapping ORF, which encodes a structurally unrelated protein - Alex. Alternative splicing of downstream exons is also observed, which results in different forms of the stimulatory G-protein alpha subunit, a key element of the classical signal transduction pathway linking receptor-ligand interactions with the activation of adenylyl cyclase and a variety of cellular reponses. Multiple transcript variants encoding different isoforms have been found for this gene. Mutations in this gene result in pseudohypoparathyroidism type 1a, pseudohypoparathyroidism type 1b, Albright hereditary osteodystrophy, pseudopseudohypoparathyroidism, McCune-Albright syndrome, progressive osseus heteroplasia, polyostotic fibrous dysplasia of bone, and some pituitary tumors. [provided by RefSeq, Aug 2012]

GNAS (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 5 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. Fraction of 0.00928 CDS is truncated, and there are 3 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 20-58910818-G-T is Pathogenic according to our data. Variant chr20-58910818-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 29745.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr20-58910818-G-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNAS	NM_000516.7	c.1174G>T	p.Glu392*	stop_gained	13/13	ENST00000371085.8	NP_000507.1
GNAS	NM_016592.5	c.*1080G>T		3_prime_UTR_variant	13/13	ENST00000371075.7	NP_057676.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAS	ENST00000371085.8	c.1174G>T	p.Glu392*	stop_gained	13/13	1	NM_000516.7	ENSP00000360126.3
GNAS	ENST00000676826.2	c.3106G>T	p.Glu1036*	stop_gained	13/13			ENSP00000504675.2
GNAS	ENST00000371102.8	c.3061G>T	p.Glu1021*	stop_gained	12/12	5		ENSP00000360143.4
GNAS	ENST00000354359.12	c.1177G>T	p.Glu393*	stop_gained	13/13	1		ENSP00000346328.7
GNAS	ENST00000371095.7	c.1132G>T	p.Glu378*	stop_gained	12/12	1		ENSP00000360136.3
GNAS	ENST00000470512.6	c.1000G>T	p.Glu334*	stop_gained	13/13	5		ENSP00000499552.2
GNAS	ENST00000480232.6	c.1000G>T	p.Glu334*	stop_gained	14/14	5		ENSP00000499545.2
GNAS	ENST00000663479.2	c.1000G>T	p.Glu334*	stop_gained	13/13			ENSP00000499353.2
GNAS	ENST00000462499.6	c.955G>T	p.Glu319*	stop_gained	12/12	2		ENSP00000499758.2
GNAS	ENST00000467227.6	c.955G>T	p.Glu319*	stop_gained	13/13	3		ENSP00000499681.2
GNAS	ENST00000478585.6	c.955G>T	p.Glu319*	stop_gained	12/12	2		ENSP00000499762.2
GNAS	ENST00000481039.6	c.955G>T	p.Glu319*	stop_gained	12/12	5		ENSP00000499767.2
GNAS	ENST00000485673.6	c.955G>T	p.Glu319*	stop_gained	12/12	5		ENSP00000499334.2
GNAS	ENST00000488546.6	c.955G>T	p.Glu319*	stop_gained	12/12	5		ENSP00000499332.2
GNAS	ENST00000492907.6	c.955G>T	p.Glu319*	stop_gained	12/12	3		ENSP00000499443.2
GNAS	ENST00000371075.7	c.*1080G>T		3_prime_UTR_variant	13/13	1	NM_016592.5	ENSP00000360115.3
GNAS	ENST00000453292.7	c.*1035G>T		3_prime_UTR_variant	12/12	5		ENSP00000392000.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Pseudohypoparathyroidism type 1C Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jun 01, 2011

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.62	D
BayesDel_noAF	Pathogenic	0.65
CADD	Pathogenic	43
DANN	Uncertain	1.0
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.98	D
Vest4		0.70
GERP RS		5.2

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

LitVar

Other links and lift over

dbSNP: rs397514456; hg19: chr20-57485873;