ConVarT

ClinVar Data

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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

Missense Variant

Synonymous Variant

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Variant ID	Transcript ID	Alteration	Annotation	Allele C.	Allele N.	Allele F.	rsNumber	Flags	Filter
19-13210147-G-A	ENST00000264824	p.Pro277Ser	Missense Variant	0	0	0	rs751042831
19-13210154-A-C	ENST00000264824	p.Ala274Ala	Synonymous Variant	1	31290	0.000032	rs1250480024
19-13210157-G-A	ENST00000264824	p.Thr273Thr	Synonymous Variant	2	31288	0.000064	rs756741592
19-13210161-T-C	ENST00000264824	p.Gln272Arg	Missense Variant	0	0	0	rs1371238548
19-13210165-C-T	ENST00000264824	p.Glu271Lys	Missense Variant	0	0	0	rs778172606
19-13210167-A-C	ENST00000264824	p.Met270Arg	Missense Variant	0	0	0	rs745524258
19-13210168-T-G	ENST00000264824	p.Met270Leu	Missense Variant	1	31222	0.000032	rs1181775701
19-13210174-T-C	ENST00000264824	p.Ile268Val	Missense Variant	1	31208	0.000032	rs1049819430
19-13210177-G-T	ENST00000264824	p.Pro267Thr	Missense Variant	6	31220	0.000192	rs373053644
19-13210179-C-G	ENST00000264824	p.Arg266Pro	Missense Variant	0	0	0	rs749120126
19-13210180-G-A	ENST00000264824	p.Arg266Trp	Missense Variant	0	0	0	rs768595898
19-13210181-G-T	ENST00000264824	p.Ala265Ala	Synonymous Variant	0	0	0	rs774175399
19-13210190-A-G	ENST00000264824	p.Gly262Gly	Synonymous Variant	1	31082	0.000032	rs748198508		RF
19-13210192-C-T	ENST00000264824	p.Gly262Ser	Missense Variant	0	0	0	rs772046377
19-13210201-C-T	ENST00000264824	p.Gly259Ser	Missense Variant	0	0	0	rs1480041687
19-13210204-C-A	ENST00000264824	p.Asp258Tyr	Missense Variant	1	31066	0.000032	rs773488111
19-13210219-G-A	ENST00000264824	p.Pro253Ser	Missense Variant	0	0	0	rs545061070
19-13210220-C-CGCGGGCTGCGA	ENST00000264824	p.Pro253ArgfsTer27	Frameshift Variant	2	31050	0.000064	rs1457598958	lc_lof
19-13210222-CGGGCTGCGAGCGCGCTGCCGCCTCGGCCCTGCGTCCGGATCCCCG-C	ENST00000264824	p.Arg237_Pro251del	Inframe Deletion	0	0	0	rs1254827403
19-13210224-G-A	ENST00000264824	p.Pro251Leu	Missense Variant	1	31062	0.000032	rs1161021255

Showing 1 to 20 of 239 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
LYL1	P12980	Phosphorylation	134	S134-p	SRLKRRPsHCELDLA	29.94	4705347
LYL1	P12980	Phosphorylation	25	S25-p	AEMVCAPsPAPAPPP	29.94	23123586
LYL1	P12980	Phosphorylation	260	S260-p	PPADPDGsPGGAARP	29.94	25173096
LYL1	P12980	Phosphorylation	276	S276-p	KMEQTALsPEVR___	29.94	23123589
LYL1	P12980	Phosphorylation	36	S36-p	APPPKPAsPGPPQVE	29.94	15624701

Showing 1 to 5 of 5 entries

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Catalogue of Somatic Mutations in Cancer (COSMIC)

Nonstop Extension

Substitution - Coding Silent

Substitution - Missense

Unknown

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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
LYL1	ENST00000264824	05-187J3	prostate	carcinoma	23976950	c.245C>A	p.T82N	Substitution - Missense	NEUTRAL	.35198	Confirmed somatic variant	PMID: 26928463	metastasis	82
LYL1	ENST00000264824	W10T	thyroid	carcinoma	23976707	c.703G>T	p.A235S	Substitution - Missense	NEUTRAL	.16754	Confirmed somatic variant	PMID: N/A	primary	235
LYL1	ENST00000264824	GBM20-R3	central_nervous_system	glioma	23976155	c.653C>T	p.T218I	Substitution - Missense	NEUTRAL	.17151	Confirmed somatic variant	PMID: 28263318	recurrent	218
LYL1	ENST00000264824	S02120_1	lung	carcinoma	23975613	c.411G>T	p.E137D	Substitution - Missense	PATHOGENIC	.92725	Confirmed somatic variant	PMID: 26168399	primary	137
LYL1	ENST00000264824	CML025T	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	23976312	c.586A>T	p.M196L	Substitution - Missense	PATHOGENIC	.90525	Confirmed somatic variant	PMID: N/A	primary	196
LYL1	ENST00000264824	TCGA-AA-3492-01	large_intestine	carcinoma	23976498	c.501C>T	p.N167=	Substitution - coding silent	PATHOGENIC	.86731	Confirmed somatic variant	PMID: N/A	NS	167
LYL1	ENST00000264824	DCG_04	central_nervous_system	glioma	23975544	c.635C>T	p.A212V	Substitution - Missense	NEUTRAL	.27194	Confirmed somatic variant	PMID: 28852847	NS	212
LYL1	ENST00000264824	S00941_1	lung	carcinoma	23976308	c.358C>G	p.P120A	Substitution - Missense		.66976	Confirmed somatic variant	PMID: 26168399	primary	120
LYL1	ENST00000264824	TCGA-AM-5820-01	large_intestine	carcinoma	23976062	c.165G>A	p.R55=	Substitution - coding silent		.59235	Confirmed somatic variant	PMID: N/A	NS	55
LYL1	ENST00000264824	7	skin	carcinoma	23976225	c.825G>C	p.L275F	Substitution - Missense	NEUTRAL	.4761	Confirmed somatic variant	PMID: 27592799	primary	275
LYL1	ENST00000264824	T2940	large_intestine	carcinoma	23975757	c.654C>A	p.T218=	Substitution - coding silent	NEUTRAL	.15645	Confirmed somatic variant	PMID: 25344691	NS	218
LYL1	ENST00000264824	W29T	thyroid	carcinoma	23976230	c.478C>A	p.R160S	Substitution - Missense	PATHOGENIC	.93375	Confirmed somatic variant	PMID: N/A	primary	160
LYL1	ENST00000264824	TCGA-AP-A1E0-01	endometrium	carcinoma	23976632	c.340T>G	p.Y114D	Substitution - Missense	PATHOGENIC	.94841	Confirmed somatic variant	PMID: N/A	NS	114
LYL1	ENST00000264824	CSCC-2-T	skin	carcinoma	23976716	c.127G>A	p.E43K	Substitution - Missense	NEUTRAL	.18295	Confirmed somatic variant	PMID: 25303977	primary	43
LYL1	ENST00000264824	TCGA-RC-A6M4-01	liver	carcinoma	23975815	c.153C>T	p.S51=	Substitution - coding silent	NEUTRAL	.16482	Confirmed somatic variant	PMID: N/A	primary	51
LYL1	ENST00000264824	T197	large_intestine	carcinoma	23976740	c.134T>C	p.V45A	Substitution - Missense	NEUTRAL	.08984	Confirmed somatic variant	PMID: 27149842	NS	45
LYL1	ENST00000264824	TCGA-AC-A8OR-01	breast	carcinoma	23975363	c.258G>A	p.P86=	Substitution - coding silent	NEUTRAL	.03109	Confirmed somatic variant	PMID: N/A	primary	86
LYL1	ENST00000264824	131	stomach	carcinoma	23976151	c.189C>G	p.I63M	Substitution - Missense	PATHOGENIC	.92263	Confirmed somatic variant	PMID: N/A	primary	63
LYL1	ENST00000264824	TCGA-DC-6683-01	large_intestine	carcinoma	23976617	c.64T>C	p.C22R	Substitution - Missense	NEUTRAL	.10377	Confirmed somatic variant	PMID: N/A	primary	22
LYL1	ENST00000264824	151	stomach	carcinoma	23976457	c.*6C>T	p.?	Unknown	NEUTRAL	.17364	Confirmed somatic variant	PMID: N/A	primary	0

Showing 1 to 20 of 67 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
PF00010	HLH	Helix-loop-helix DNA-binding domain	151-203			Homo sapiens

List of the diseases from DisGeNET

Disease Name	Disease Category	DSI*	DPI**
Lymphoid leukemia	Neoplasms ; Hemic and Lymphatic Diseases ; Immune System Diseases ;	0.72	0.138
Leukemia, Myelocytic, Acute	Neoplasms ;	0.72	0.138
Acute Myeloid Leukemia, M1	Neoplasms ;	0.72	0.138
Acute Myeloid Leukemia (AML-M2)	Neoplasms ;	0.72	0.138
Hematopoetic Myelodysplasia	Hemic and Lymphatic Diseases ;	0.72	0.138
MYELODYSPLASTIC SYNDROME	Hemic and Lymphatic Diseases ;	0.72	0.138
NO RESULT FOUND

Description:	LYL1, basic helix-loop-helix family member [Source:RGD Symbol;Acc:1359244]
Synonyms:
Other ID(s):	ENSRNOG00000002950
Protein Accession Numbers:	NP_001007678
Statistics:	gnomAD(239) COSMIC(67) PTM(5)

Classification of Clinicial Significance of ClinVar Data