1-114713909-G-T

Position:

• chr1-114713909-G-T

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1 PM2 PM5 PP3_Moderate PP5

The NM_002524.5(NRAS):​c.181C>A​(p.Gln61Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q61H) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: NRAS NM_002524.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:1 O:2
• Conservation: PhyloP100: 9.87

Genes affected

NRAS (HGNC:7989): (NRAS proto-oncogene, GTPase) This is an N-ras oncogene encoding a membrane protein that shuttles between the Golgi apparatus and the plasma membrane. This shuttling is regulated through palmitoylation and depalmitoylation by the ZDHHC9-GOLGA7 complex. The encoded protein, which has intrinsic GTPase activity, is activated by a guanine nucleotide-exchange factor and inactivated by a GTPase activating protein. Mutations in this gene have been associated with somatic rectal cancer, follicular thyroid cancer, autoimmune lymphoproliferative syndrome, Noonan syndrome, and juvenile myelomonocytic leukemia. [provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 3 uncertain in NM_002524.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr1-114713908-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 13900.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.896
• PP5: Variant 1-114713909-G-T is Pathogenic according to our data. Variant chr1-114713909-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 73058.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=2, other=1}. Variant chr1-114713909-G-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NRAS	NM_002524.5	c.181C>A	p.Gln61Lys	missense_variant	3/7	ENST00000369535.5	NP_002515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NRAS	ENST00000369535.5	c.181C>A	p.Gln61Lys	missense_variant	3/7	1	NM_002524.5	ENSP00000358548.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1460146 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 726204

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:1 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Large congenital melanocytic nevus Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	May 21, 2020	A heterozygous missense variant was identified, NM_002524.3(NRAS):c.181C>A in exon 3 of the NRAS gene. This substitution is predicted to create a minor amino acid change from a glutamine to a lysine at position 61 of the protein; NP_002515.1(NRAS):p.(Gln61Lys). The glutamine at this position has very high conservation (100 vertebrates, UCSC), and is located within the switch II region (Cirstea, I. C. et al. (2010)). In silico software predicts this variant to be damaging (PolyPhen2, PROVEAN, MutationAssessor, FATHMM). The variant is not present in the gnomAD population database. This variant has been previously reported as pathogenic in multiple patients with congenital melanocytic naevi (ClinVar, Kinsler, V. A. et al. (2013)). In addition, functional studies show that this variant causes melanocyte survival and growth in the epidermis (Li, A. et al. (2012)). Different variants in the same codon resulting in changes to histidine, leucine, arginine, proline and glutamic acid, have also been reported as pathogenic (ClinVar). Based on information available at the time of curation, this variant has been classified as PATHOGENIC. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Sep 01, 2013	- -

Vascular Tumors Including Pyogenic Granuloma Pathogenic:1

Likely pathogenic, no assertion criteria provided

literature only

Yale Center for Mendelian Genomics, Yale University

Feb 19, 2015

- -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2018

- -

Neurocutaneous melanocytosis Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Sep 01, 2013

- -

RASopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

curation

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2018

This sequence change replaces glutamine with lysine at codon 61 of the NRAS protein (p.Gln61Lys). The glutamine residue is highly conserved and there is a small physicochemical difference between glutamine and lysine. This variant is not present in population databases (ExAC no frequency). While this variant has been published in the literature (PMID: 23392294), it has not been reported in the germline of an individual with NRAS-related disease. ClinVar contains an entry for this variant (Variation ID: 73058). This variant has been reported as a recurrent variant in melanoma tumors (PMID: 23392294), colorectal tumors (PMID: 27050078, 23400451), thyroid tumors (PMID: 28780248), squamous cell lung tumors (PMID: 25348872), neuroblastoma tumors (PMID: 26821351), and gynecological tumors (PMID: 24671188). Experimental studies have shown that this missense change p.Gln61Lys, results in cytoskeletal changes in melanocyte cell lines, reduces apoptosis, and results in hyperpigmented skin in transgenic mice who develop cutaneous metastasizing melanoma (PMID: 22718121, 18668139, 15899789). However, in a thyroid epithelial cell line, this variant alone resulted in zero tumor instances (PMID: 10821536). In zebrafish, expression of human NRAS p.Q61K in melanocytes results in the growth of pigmented lesions that rarely progress to melanoma. (PMID: 24148783). 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. -

Neoplasm Other:1

-, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Jul 31, 2024

- -

Ras Inhibitor response Other:1

drug response, no assertion criteria provided

clinical testing

Oxford Haemato-Oncology Service, Oxford University Hospitals NHS Foundation Trust

Nov 27, 2017

- Likely response to RAS inhibitors.

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.36
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.68	D
Eigen	Pathogenic	0.96
Eigen_PC	Pathogenic	0.90
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.93	D
M_CAP	Uncertain	0.10	D
MetaRNN	Pathogenic	0.90	D
MetaSVM	Uncertain	0.70	D
MutationAssessor	Pathogenic	3.4	M
PrimateAI	Pathogenic	0.88	D
PROVEAN	Uncertain	-3.4	D
REVEL	Pathogenic	0.84
Sift	Uncertain	0.0090	D
Sift4G	Uncertain	0.017	D
Polyphen		0.95	P
Vest4		0.75
MutPred		0.73		Gain of ubiquitination at Q61 (P = 0.0247);
MVP		0.93
MPC		1.2
ClinPred		0.98	D
GERP RS		5.1
Varity_R		0.91
gMVP		0.85

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: rs121913254; hg19: chr1-115256530; COSMIC: COSV54736310; COSMIC: COSV54736310;