ConVarT

NOL3 (GeneID: 8996) | Homo sapiens

Description:	nucleolar protein 3 [Source:HGNC Symbol;Acc:HGNC:7869]
Synonyms:	NOP, ARC, MYP, NOP30, FCM
Other ID(s):	HGNC:7869, ENSG00000140939
Protein Accession Numbers:	NP_001263248, ENST00000565560, NP_001263238, ENST00000564053, ENST00000568146, ENST00000432069, NP_001263241, ENST00000564992, NP_001263236, ENST00000563439, NP_003937, ENST00000268605, ENST00000566871, NP_001263240, ENST00000564860, NP_001171986, ENST00000563258
Statistics:	ClinVar(20) gnomAD(550) COSMIC(102) PTM(8)

ClinVar Pathogenicity of Variations

Benign

Pathogenic

VUS

∙ Please click the name of species for the protein accession number used in the alignment.
∙ A p letter used as a pointer to positions of post translational modifications in human.
∙ Protein domains illustrated above belong to Homo sapiens (Human).
∙ ClinVar stacked bar chart represents whole protein isoforms of the gene. Please, check the other protein isoforms of the gene below.
∙ If more than one transcripts below are active (with blue background color), it means all the active transcripts have the same sequence.
ENST00000268605 You are here now! ENST00000432069 You are here now! ENST00000563258 ENST00000563439 ENST00000564053 ENST00000564860 ENST00000564992 ENST00000565560 ENST00000566871 ENST00000568146 NP_001171986 NP_001263236 You are here now! NP_001263238 You are here now! NP_001263240 NP_001263241 You are here now! NP_001263248 NP_003937 You are here now!

ClinVar Data

Show entries

Variation ID	Allele ID	RS Number	Variant Type	Record	Alteration	Clinicial Sig.	Last Update	Phenotypes	Cytogenetic	Review Status	RCV Acc.N.

gnomAD

Frameshift Variant

Inframe Deletion

Inframe Insertion

Missense Variant

Splice Region Variant

Start Lost

Stop Gained

Stop Lost

Synonymous Variant

Show entries

Variant ID	Transcript ID	Alteration	Annotation	Allele C.	Allele N.	Allele F.	rsNumber	Flags
16-67208073-A-G	ENST00000268605	p.Met1?	Start Lost	0	0	0	rs1418616403
16-67208073-A-G	ENST00000432069	p.Met1?	Start Lost	0	0	0	rs1418616403
16-67208076-G-GGCAAC	ENST00000268605	p.Gln5ThrfsTer221	Frameshift Variant	0	0	0	rs1295779091
16-67208076-G-GGCAAC	ENST00000432069	p.Gln5ThrfsTer221	Frameshift Variant	0	0	0	rs1295779091
16-67208078-C-A	ENST00000268605	p.Gly2Gly	Synonymous Variant	0	0	0	rs1383519320
16-67208078-C-A	ENST00000432069	p.Gly2Gly	Synonymous Variant	0	0	0	rs1383519320
16-67208081-C-CAAT	ENST00000268605	p.Asn3dup	Inframe Insertion	0	0	0	rs1235623788
16-67208081-C-CAAT	ENST00000432069	p.Asn3dup	Inframe Insertion	0	0	0	rs1235623788
16-67208081-C-T	ENST00000268605	p.Asn3Asn	Synonymous Variant	0	0	0	rs1235623788
16-67208081-C-T	ENST00000432069	p.Asn3Asn	Synonymous Variant	0	0	0	rs1235623788
16-67208082-G-A	ENST00000268605	p.Ala4Thr	Missense Variant	1	31398	0.000032	rs563320532	mnv
16-67208082-G-A	ENST00000432069	p.Ala4Thr	Missense Variant	1	31398	0.000032	rs563320532	mnv
16-67208082-GCGCAGGAGC-G	ENST00000268605	p.Ala4_Arg7delinsGly	Inframe Deletion	0	0	0	rs563320532
16-67208082-GCGCAGGAGC-G	ENST00000432069	p.Ala4_Arg7delinsGly	Inframe Deletion	0	0	0	rs563320532
16-67208083-C-A	ENST00000268605	p.Ala4Glu	Missense Variant	1	31408	0.000032	rs576743079	mnv
16-67208083-C-A	ENST00000432069	p.Ala4Glu	Missense Variant	1	31408	0.000032	rs576743079	mnv
16-67208086-A-T	ENST00000268605	p.Gln5Leu	Missense Variant	1	31400	0.000032	rs545720249
16-67208086-A-T	ENST00000432069	p.Gln5Leu	Missense Variant	1	31400	0.000032	rs545720249
16-67208088-G-T	ENST00000268605	p.Glu6Ter	Stop Gained	0	0	0	rs779917958
16-67208088-G-T	ENST00000432069	p.Glu6Ter	Stop Gained	0	0	0	rs779917958

Showing 1 to 20 of 550 entries

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Post-translational Modifications (PTMs)

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Gene Name	ACC ID	PTM Type	Position	Mod-rsd	Site +/-7 Aa	Mw_kd	Site grpID
NOL3	O60936	Phosphorylation	104	S104-p	GPGYRDRsyDPPCPG	22.63	18006736
NOL3	O60936	Phosphorylation	105	Y105-p	PGYRDRsyDPPCPGH	22.63	4774952
NOL3	O60936	Phosphorylation	114	T114-p	PPCPGHWtPEAPGsG	22.63	477982
NOL3	O60936	Phosphorylation	120	S120-p	WtPEAPGsGttCPGL	22.63	18006739
NOL3	O60936	Phosphorylation	122	T122-p	PEAPGsGttCPGLPR	22.63	18006742
NOL3	O60936	Phosphorylation	123	T123-p	EAPGsGttCPGLPRA	22.63	18006745
NOL3	O60936	Phosphorylation	149	T149-p	SEAVQSGtPEEPEPE	22.63	448618
NOL3	O60936	Phosphorylation	162	S162-p	PELEAEAsKEAEPEP	22.63	36129749

Showing 1 to 8 of 8 entries

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Catalogue of Somatic Mutations in Cancer (COSMIC)

Deletion - In Frame

Substitution - Coding Silent

Substitution - Missense

Substitution - Nonsense

Unknown

Show entries

Gene Name	Transcript ID	Sample name	Primary Site	Primary Histology	Mutation ID	Mutation CDS	Mutation Aa	Mutation Desc.	FATHMM Prediction	FATHMM Score	Mutation Somatic Status	PUBMED PMID	Tumor Origin	Position
NOL3_ENST00000268605	ENST00000268605	5-VS054-T1	skin	carcinoma	23512658	c.323C>T	p.P108L	Substitution - Missense	NEUTRAL	.13358	Confirmed somatic variant	PMID: 26950094	NS	108
NOL3_ENST00000268605	ENST00000268605	2834130	skin	malignant_melanoma	96323086	c.316G>T	p.D106Y	Substitution - Missense	NEUTRAL	.43019	Variant of unknown origin	PMID: 28296713	primary	106
NOL3_ENST00000268605	ENST00000268605	2834130	skin	malignant_melanoma	96323085	c.185T>C	p.L62P	Substitution - Missense		.67767	Variant of unknown origin	PMID: 28296713	primary	62
NOL3_ENST00000268605	ENST00000268605	2434065	haematopoietic_and_lymphoid_tissue	lymphoid_neoplasm	23512888	c.-36G>C	p.?	Unknown	NEUTRAL	.03017	Confirmed somatic variant	PMID: 26192917	NS	0
NOL3_ENST00000268605	ENST00000268605	DCG_04	central_nervous_system	glioma	96323093	c.514G>C	p.E172Q	Substitution - Missense		.58606	Confirmed somatic variant	PMID: 28852847	NS	172
NOL3_ENST00000268605	ENST00000268605	GCTK_349_T	stomach	carcinoma	23512498	c.507_512del	p.P173_E174del	Deletion - In frame			Confirmed somatic variant	PMID: N/A	primary	173
NOL3_ENST00000268605	ENST00000268605	TCGA-06-0241	central_nervous_system	glioma	23512617	c.550G>A	p.E184K	Substitution - Missense	NEUTRAL	.2752	Confirmed somatic variant	PMID: 23917401	NS	184
NOL3_ENST00000268605	ENST00000268605	H1648	lung	carcinoma	23513143	c.37G>C	p.D13H	Substitution - Missense	NEUTRAL	.16605	Variant of unknown origin	PMID: 29681454	NS	13
NOL3_ENST00000268605	ENST00000268605	GCTK_519_T	stomach	carcinoma	23512551	c.438A>G	p.Q146=	Substitution - coding silent	NEUTRAL	.0331	Confirmed somatic variant	PMID: N/A	primary	146
NOL3_ENST00000268605	ENST00000268605	T207430	large_intestine	carcinoma	23512915	c.15G>T	p.Q5H	Substitution - Missense	NEUTRAL	.31644	Confirmed somatic variant	PMID: 27149842	NS	5
NOL3_ENST00000268605	ENST00000268605	Thyroid-CN-WZ046T	thyroid	carcinoma	23512955	c.214G>T	p.A72S	Substitution - Missense		.6792	Confirmed somatic variant	PMID: N/A	primary	72
NOL3_ENST00000268605	ENST00000268605	13	skin	carcinoma	23512869	c.83G>T	p.G28V	Substitution - Missense	NEUTRAL	.46087	Confirmed somatic variant	PMID: 27592799	primary	28
NOL3_ENST00000268605	ENST00000268605	W23T	thyroid	carcinoma	23512520	c.*235G>T	p.?	Unknown	NEUTRAL	.0161	Confirmed somatic variant	PMID: N/A	primary	0
NOL3_ENST00000268605	ENST00000268605	ESCC_BICR_024T	oesophagus	carcinoma	23512741	c.610G>A	p.E204K	Substitution - Missense	NEUTRAL	.10307	Confirmed somatic variant	PMID: N/A	primary	204
NOL3_ENST00000268605	ENST00000268605	TCGA-D7-A4YY-01	stomach	carcinoma	23513344	c.328C>A	p.P110T	Substitution - Missense	NEUTRAL	.12249	Confirmed somatic variant	PMID: N/A	NS	110
NOL3_ENST00000268605	ENST00000268605	PD26928a	skin	malignant_melanoma	23513130	c.57G>A	p.L19=	Substitution - coding silent	NEUTRAL	.23514	Confirmed somatic variant	PMID: 30664638	primary	19
NOL3_ENST00000268605	ENST00000268605	TCGA-D3-A2JK-06	skin	malignant_melanoma	96323117	c.415C>A	p.P139T	Substitution - Missense	NEUTRAL	.0427	Confirmed somatic variant	PMID: N/A	NS	139
NOL3_ENST00000268605	ENST00000268605	AOCS-094-1-1	ovary	carcinoma	96323113	c.295+51G>C	p.?	Unknown	NEUTRAL	.11898	Confirmed somatic variant	PMID: N/A	NS	0
NOL3_ENST00000268605	ENST00000268605	ESCC_00396	oesophagus	carcinoma	23512541	c.293C>A	p.P98Q	Substitution - Missense	NEUTRAL	.10071	Confirmed somatic variant	PMID: 27058444	NS	98
NOL3_ENST00000268605	ENST00000268605	1T65	oesophagus	carcinoma	23513400	c.616G>A	p.E206K	Substitution - Missense		.6663	Confirmed somatic variant	PMID: N/A	primary	206

Showing 1 to 20 of 102 entries

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dbSNP

Gene ID	Transcript ID	Consequence	Position	HGVSp	Impact

Protein Domains (PFAM)

Pfam Domain	Domain Name	Description	Positions	Clan	Clan Name	Organism
NO RESULT FOUND
PF00619	CARD	Caspase recruitment domain	9-96	CL0041	Death	Homo sapiens

List of the diseases from DisGeNET

Disease Name	Disease Category	DSI*	DPI**
Mitochondrial Diseases	Nutritional and Metabolic Diseases ;	0.667	0.552
Electron Transport Chain Deficiencies, Mitochondrial	Nutritional and Metabolic Diseases ;	0.667	0.552
Oxidative Phosphorylation Deficiencies	Nutritional and Metabolic Diseases ;	0.667	0.552
Mitochondrial Respiratory Chain Deficiencies	Nutritional and Metabolic Diseases ;	0.667	0.552
MYOCLONUS, FAMILIAL CORTICAL	N/A	0.667	0.552
NO RESULT FOUND

Classification of Clinicial Significance of ClinVar Data