Variant classification summary

NM_000516.5:c.601C>T

GNAS · NP_000507.1:p.(Arg201Cys) · NM_000516.5

GRCh37: chr20:57484420 C>T · GRCh38: chr20:58909365 C>T

Gene: GNAS Transcript: NM_000516.5

Final call

Likely Pathogenic

PS3 strong PM1 moderate PM2 supporting PP3 supporting

Variant details

Gene

GNAS

Transcript

NM_000516.5

Protein

NP_000507.1:p.(Arg201Cys)

gnomAD AF

4.958165478772854e-06 (v4.1)

ClinVar

Pathogenic

OncoKB

Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

Functional studies demonstrate that c.601C>T (p.Arg201Cys) constitutively activates Gsα by inhibiting GTPase activity, leading to autonomous cAMP production and downstream tumorigenesis (PS3_Strong).

2

Arg201 is a well-established mutational hotspot within the GTPase domain of Gsα, where multiple substitutions (Cys, His, Ser, Gly, Leu) cause constitutive activation of adenylyl cyclase (PM1_Moderate).

3

The variant is absent from gnomAD v2.1 (0/251,470 alleles) and extremely rare in gnomAD v4.1 (8/1,613,500; AF=4.96×10⁻⁶), far below the 0.1% threshold for rare variant support (PM2_Supporting).

4

Multiple in silico tools predict a deleterious effect, with a REVEL score of 0.943 indicating a high likelihood of pathogenicity (PP3_Supporting).

5

Applying generic ACMG/AMP 2015 combination rules: 1 Strong (PS3) + 1 Moderate (PM1) + 2 Supporting (PM2, PP3) supports classification as Likely Pathogenic.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	c.601C>T (p.Arg201Cys) is a missense variant that does not fall into any null-variant bucket (nonsense, frameshift, or canonical ±1,2 splice consensus) required for PVS1 applicability under the ClinGen SVI PVS1 decision tree (PMC6185798).	pvs1_generic_framework
PS1	N/A	No evidence of a different nucleotide change producing the same p.Arg201Cys substitution was identified. The only known nucleotide change yielding R201C is c.601C>T (CGT→TGT).
PS2	N/A	McCune-Albright syndrome is a postzygotic somatic mosaic disorder; the variant is not observed as a germline de novo event with confirmed maternity/paternity. PS2 applies only to germline de novo variants.
PS3	Met	The R201C variant has been directly tested in two independent functional studies. PMID:20531296 demonstrated that GNAS R201C promotes intestinal tumorigenesis in an Apc(Min/+) mouse model through constitutive activation of Wnt and ERK1/2 MAPK pathways. PMID:2549426 demonstrated that R201C inhibits GTPase activity of Gsα, leading to constitutive activation of adenylyl cyclase and autonomous cAMP production. Both studies provide unequivocal functional evidence of a gain-of-function effect.	PMID:20531296 PMID:2549426
PS4	Not met	PS4 requires statistically significant enrichment in affected individuals versus controls. While the variant has been observed in multiple McCune-Albright syndrome cases (PMID:15126527 reported R201C in 15/49 mutation-positive patients), formal case-control statistics are not available and the postzygotic somatic mosaic nature of this disorder precludes standard PS4 application.	PMID:15126527 PMID:17873334
PS5	N/A	PS5 applies to de novo germline variants with confirmed maternity/paternity but without identity-by-descent confirmation. No such evidence exists for this postzygotic somatic mutation.
PM1	Met	The variant alters Arg201, a well-established mutational hotspot in the GTPase domain of Gsα. Cancer Hotspots identifies this residue as statistically significant. The Gsα GTPase domain is a critical functional domain where substitutions at Arg201 (R201C, R201H, R201S, R201G, R201L) constitutively activate adenylyl cyclase by impairing GTP hydrolysis. The variant lies within a well-characterized functional domain without benign variation.	PMID:20531296 PMID:2549426 oncokb
PM2	Met	This variant is absent from gnomAD v2.1 exomes (0/251,470 alleles) and present at extremely low frequency in gnomAD v4.1 (8/1,613,500 alleles; AF=4.96×10⁻⁶), well below the PM2 threshold of <0.1%. The rare alleles in v4.1 are consistent with somatic mosaicism or technical artifact rather than germline variation.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 applies to novel missense variants at an amino acid residue where a different pathogenic missense change has been established. R201C (c.601C>T) is itself an established pathogenic variant — it is not a novel change at codon 201. The classic PM5 paradigm is directed at previously unreported missense changes, not well-characterized pathogenic variants.
PM6	N/A	PM6 requires a de novo germline observation with confirmed maternity/paternity. McCune-Albright syndrome is caused by postzygotic somatic mutations; no germline de novo observation exists for this variant.
PP1	Not met	No segregation data are available in the reviewed literature. McCune-Albright syndrome is a postzygotic somatic mosaic disorder not transmitted through families, making PP1 inapplicable.
PP2	Not met	PP2 requires a gene with a low rate of benign missense variation (high missense Z-score) where missense variants are a common mechanism of disease. While codon 201 is a known hotspot, gene-level missense constraint data sufficient for PP2 application were not available in the evidence brief.
PP3	Met	Multiple in silico tools predict a damaging effect. REVEL score is 0.943 (highly deleterious), BayesDel score is 0.543. SpliceAI predicts no splice impact (max delta=0.00), consistent with a missense effect rather than splicing defect. The high REVEL score supports a pathogenic role.	revel bayesdel spliceai
PP4	Not met	PP4 requires the patient's phenotype or family history to be highly specific for the gene's disease spectrum. No patient-specific clinical data were provided for evaluation.
PP5	Not met	ClinVar classifies this variant as Pathogenic with review status of 'criteria provided, single submitter' (1-star). Under generic ACMG/AMP, PP5 may be applied when a reputable source classifies a variant as pathogenic but the evidence is not available for independent evaluation. In this case, the evidence underlying the ClinVar classifications has been independently evaluated through the cited PMIDs, and the review status does not meet the expert panel (3-star) threshold for the PP5 override rule. The 5 clinical laboratory classifications as Pathogenic are consistent with but not additive to the independently assessed criteria.	clinvar
BA1	Not met	The variant is absent from gnomAD v2.1 and extremely rare in gnomAD v4.1 (AF=4.96×10⁻⁶). This is well below the BA1 threshold of >1% allele frequency.	gnomad_v2 gnomad_v4
BS1	Not met	The variant's population frequency (AF=4.96×10⁻⁶ in gnomAD v4.1; absent in v2.1) is well below the BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4
BS2	Not met	Eight alleles are observed in gnomAD v4.1, but this variant causes McCune-Albright syndrome — a postzygotic somatic mosaic disorder, not a germline condition with full penetrance expected at an early age. The very low allele counts in gnomAD are consistent with somatic mosaicism or sequencing artifact and do not constitute observation in healthy adult germline carriers.	gnomad_v4
BS3	Not met	Published functional studies (PMID:20531296, PMID:2549426) demonstrate a gain-of-function activating effect — constitutive adenylyl cyclase stimulation and tumor promotion — not a benign effect. BS3 requires evidence that the variant does NOT alter protein function, which is contradicted by the functional data.	PMID:20531296 PMID:2549426
BS4	Not met	No segregation data demonstrating lack of cosegregation with disease are available. McCune-Albright syndrome is a postzygotic somatic mosaic disorder not transmitted in families, making BS4 inapplicable.
BP1	Not met	BP1 applies to missense variants in genes where only truncating variants cause disease. GNAS has both loss-of-function (pseudohypoparathyroidism, PHP1A) and gain-of-function (McCune-Albright syndrome) disease mechanisms. The BP1 exclusion does not apply.
BP2	Not met	No evidence of this variant observed in trans with a known pathogenic variant in GNAS for a recessive disorder. McCune-Albright syndrome is a dominant-acting somatic mosaic disorder.
BP3	N/A	Variant is a single-nucleotide missense substitution, not an in-frame deletion/insertion.
BP4	Not met	Multiple in silico tools predict a damaging effect: REVEL score 0.943 (highly deleterious), BayesDel score 0.543. No computational evidence supports a benign interpretation. BP4 is contradicted.	revel bayesdel
BP5	Not met	BP5 requires a strong benign criterion to be met AND an alternative molecular basis for disease to be identified. Neither condition is satisfied for this variant.
BP6	Not met	ClinVar classifies this variant as Pathogenic, not Benign or Likely Benign. BP6 applies only when a reputable source classifies a variant as benign.	clinvar
BP7	N/A	c.601C>T is a missense variant (p.Arg201Cys), not a synonymous variant with no predicted splice impact. BP7 applies exclusively to synonymous variants.

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