Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	90678
Gene name	Leucine rich repeat and sterile alpha motif containing 1
Gene symbol	LRSAM1
Synonyms (NCBI Gene)	CMT2PRIFLETAL
Chromosome	9
Chromosome location	9q33.3-q34.11
Summary	This gene encodes a ring finger protein involved in a variety of functions, including regulation of signaling pathways and cell adhesion, mediation of self-ubiquitylation, and involvement in cargo sorting during receptor endocytosis. Mutations in this gen

Show/Hide all (22)

SNP ID	Visualize variation	Clinical significance	Consequence
rs56380300	A>G	Likely-benign, benign-likely-benign, conflicting-interpretations-of-pathogenicity, not-provided	Missense variant, non coding transcript variant, coding sequence variant
rs117692127	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, non coding transcript variant, 5 prime UTR variant, missense variant
rs138226428	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs148059394	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs151323851	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs387907032	G>A,C	Pathogenic	Synonymous variant, missense variant, non coding transcript variant, coding sequence variant
rs746455518	T>C,G	Likely-pathogenic	Splice donor variant
rs749012928	T>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, intron variant
rs756880678	G>A	Pathogenic, conflicting-interpretations-of-pathogenicity	Splice acceptor variant
rs759312530	T>C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs775965001	->C	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs786200930	->GC	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs876661208	TGGAGGTGCAGGC>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs876661247	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs879253755	T>C	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs879254056	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs886041051	G>A	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs1315010600	->A	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1345228128	C>G,T	Pathogenic	Non coding transcript variant, stop gained, 5 prime UTR variant, synonymous variant, coding sequence variant
rs1554763035	A>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1564287871	->CCACTGCGCACCTGCCCGCTGTGCCGCCAG	Pathogenic	Non coding transcript variant, coding sequence variant, inframe insertion
rs1588132672	AG>-	Pathogenic	Intron variant, non coding transcript variant, coding sequence variant, frameshift variant

123

Show/Hide all (123)

miRTarBase ID	miRNA	Experiments	Reference
MIRT718866	hsa-miR-4667-3p	HITS-CLIP	19536157
MIRT718865	hsa-miR-5088-3p	HITS-CLIP	19536157
MIRT718864	hsa-miR-660-3p	HITS-CLIP	19536157
MIRT718863	hsa-miR-370-3p	HITS-CLIP	19536157
MIRT718862	hsa-miR-6893-3p	HITS-CLIP	19536157
MIRT718861	hsa-miR-6734-3p	HITS-CLIP	19536157
MIRT718860	hsa-miR-4287	HITS-CLIP	19536157
MIRT718859	hsa-miR-4685-3p	HITS-CLIP	19536157
MIRT718858	hsa-miR-1976	HITS-CLIP	19536157
MIRT718857	hsa-miR-4755-3p	HITS-CLIP	19536157
MIRT718856	hsa-miR-4290	HITS-CLIP	19536157
MIRT718855	hsa-miR-7106-3p	HITS-CLIP	19536157
MIRT718854	hsa-miR-188-3p	HITS-CLIP	19536157
MIRT718853	hsa-miR-1260a	HITS-CLIP	19536157
MIRT718852	hsa-miR-1260b	HITS-CLIP	19536157
MIRT718851	hsa-miR-3156-3p	HITS-CLIP	19536157
MIRT718850	hsa-miR-6810-3p	HITS-CLIP	19536157
MIRT718866	hsa-miR-4667-3p	HITS-CLIP	19536157
MIRT718865	hsa-miR-5088-3p	HITS-CLIP	19536157
MIRT718864	hsa-miR-660-3p	HITS-CLIP	19536157
MIRT718863	hsa-miR-370-3p	HITS-CLIP	19536157
MIRT718862	hsa-miR-6893-3p	HITS-CLIP	19536157
MIRT718861	hsa-miR-6734-3p	HITS-CLIP	19536157
MIRT718860	hsa-miR-4287	HITS-CLIP	19536157
MIRT718859	hsa-miR-4685-3p	HITS-CLIP	19536157
MIRT718858	hsa-miR-1976	HITS-CLIP	19536157
MIRT718857	hsa-miR-4755-3p	HITS-CLIP	19536157
MIRT718856	hsa-miR-4290	HITS-CLIP	19536157
MIRT718855	hsa-miR-7106-3p	HITS-CLIP	19536157
MIRT718854	hsa-miR-188-3p	HITS-CLIP	19536157
MIRT718853	hsa-miR-1260a	HITS-CLIP	19536157
MIRT718852	hsa-miR-1260b	HITS-CLIP	19536157
MIRT718851	hsa-miR-3156-3p	HITS-CLIP	19536157
MIRT718850	hsa-miR-6810-3p	HITS-CLIP	19536157
MIRT1121126	hsa-miR-1285	CLIP-seq
MIRT1121127	hsa-miR-1343	CLIP-seq
MIRT1121128	hsa-miR-2110	CLIP-seq
MIRT1121129	hsa-miR-3179	CLIP-seq
MIRT1121130	hsa-miR-3187-5p	CLIP-seq
MIRT1121131	hsa-miR-3202	CLIP-seq
MIRT1121132	hsa-miR-34a	CLIP-seq
MIRT1121133	hsa-miR-34c-5p	CLIP-seq
MIRT1121134	hsa-miR-4271	CLIP-seq
MIRT1121135	hsa-miR-4283	CLIP-seq
MIRT1121136	hsa-miR-4488	CLIP-seq
MIRT1121137	hsa-miR-449a	CLIP-seq
MIRT1121138	hsa-miR-449b	CLIP-seq
MIRT1121139	hsa-miR-4697-5p	CLIP-seq
MIRT1121140	hsa-miR-4725-3p	CLIP-seq
MIRT1121141	hsa-miR-4747-5p	CLIP-seq
MIRT1121142	hsa-miR-491-5p	CLIP-seq
MIRT1121143	hsa-miR-612	CLIP-seq
MIRT1121144	hsa-miR-1255a	CLIP-seq
MIRT1121145	hsa-miR-1255b	CLIP-seq
MIRT1121146	hsa-miR-185	CLIP-seq
MIRT1121147	hsa-miR-221	CLIP-seq
MIRT1121148	hsa-miR-222	CLIP-seq
MIRT1121149	hsa-miR-2278	CLIP-seq
MIRT1121150	hsa-miR-296-5p	CLIP-seq
MIRT1121151	hsa-miR-3126-5p	CLIP-seq
MIRT1121152	hsa-miR-3150b-3p	CLIP-seq
MIRT1121153	hsa-miR-3173-3p	CLIP-seq
MIRT1121154	hsa-miR-3663-3p	CLIP-seq
MIRT1121155	hsa-miR-4306	CLIP-seq
MIRT1121156	hsa-miR-4428	CLIP-seq
MIRT1121157	hsa-miR-4459	CLIP-seq
MIRT1121158	hsa-miR-4532	CLIP-seq
MIRT1121159	hsa-miR-4644	CLIP-seq
MIRT1121160	hsa-miR-4689	CLIP-seq
MIRT1121161	hsa-miR-4722-5p	CLIP-seq
MIRT1121162	hsa-miR-4752	CLIP-seq
MIRT1121163	hsa-miR-4779	CLIP-seq
MIRT1121164	hsa-miR-4784	CLIP-seq
MIRT1121165	hsa-miR-4802-3p	CLIP-seq
MIRT1121166	hsa-miR-490-5p	CLIP-seq
MIRT1121167	hsa-miR-555	CLIP-seq
MIRT2264743	hsa-miR-1207-3p	CLIP-seq
MIRT2264744	hsa-miR-127-3p	CLIP-seq
MIRT2264745	hsa-miR-15a	CLIP-seq
MIRT2264746	hsa-miR-15b	CLIP-seq
MIRT2264747	hsa-miR-16	CLIP-seq
MIRT2264748	hsa-miR-1827	CLIP-seq
MIRT1121146	hsa-miR-185	CLIP-seq
MIRT2264749	hsa-miR-195	CLIP-seq
MIRT1121147	hsa-miR-221	CLIP-seq
MIRT1121148	hsa-miR-222	CLIP-seq
MIRT1121149	hsa-miR-2278	CLIP-seq
MIRT1121151	hsa-miR-3126-5p	CLIP-seq
MIRT2264750	hsa-miR-3150a-3p	CLIP-seq
MIRT1121153	hsa-miR-3173-3p	CLIP-seq
MIRT2264751	hsa-miR-3175	CLIP-seq
MIRT2264752	hsa-miR-3192	CLIP-seq
MIRT2264753	hsa-miR-3612	CLIP-seq
MIRT2264754	hsa-miR-3689a-3p	CLIP-seq
MIRT2264755	hsa-miR-3689c	CLIP-seq
MIRT2264756	hsa-miR-370	CLIP-seq
MIRT2264757	hsa-miR-424	CLIP-seq
MIRT1121155	hsa-miR-4306	CLIP-seq
MIRT2264758	hsa-miR-4314	CLIP-seq
MIRT1121156	hsa-miR-4428	CLIP-seq
MIRT1121157	hsa-miR-4459	CLIP-seq
MIRT1121159	hsa-miR-4644	CLIP-seq
MIRT2264759	hsa-miR-4667-5p	CLIP-seq
MIRT2264760	hsa-miR-4700-5p	CLIP-seq
MIRT1121161	hsa-miR-4722-5p	CLIP-seq
MIRT2264761	hsa-miR-4728-5p	CLIP-seq
MIRT1121162	hsa-miR-4752	CLIP-seq
MIRT1121163	hsa-miR-4779	CLIP-seq
MIRT1121165	hsa-miR-4802-3p	CLIP-seq
MIRT2264762	hsa-miR-497	CLIP-seq
MIRT1121167	hsa-miR-555	CLIP-seq
MIRT2264763	hsa-miR-637	CLIP-seq
MIRT2264764	hsa-miR-650	CLIP-seq
MIRT2264765	hsa-miR-922	CLIP-seq
MIRT2264766	hsa-miR-939	CLIP-seq
MIRT1121146	hsa-miR-185	CLIP-seq
MIRT1121149	hsa-miR-2278	CLIP-seq
MIRT1121151	hsa-miR-3126-5p	CLIP-seq
MIRT1121155	hsa-miR-4306	CLIP-seq
MIRT1121157	hsa-miR-4459	CLIP-seq
MIRT1121159	hsa-miR-4644	CLIP-seq
MIRT1121161	hsa-miR-4722-5p	CLIP-seq
MIRT1121162	hsa-miR-4752	CLIP-seq

Show/Hide all (22)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000209	Process	Protein polyubiquitination	IDA	18077552
GO:0004842	Function	Ubiquitin-protein transferase activity	IDA	15256501, 18077552
GO:0005515	Function	Protein binding	IPI	15256501, 16189514, 16713569, 18077552, 19549727, 19690564, 21044950, 23245322, 25260751, 25416956, 25484098, 27615052, 32296183, 32814053, 33961781
GO:0005737	Component	Cytoplasm	IDA	15256501, 18077552
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA
GO:0006914	Process	Autophagy	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IDA	15256501
GO:0016567	Process	Protein ubiquitination	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0030163	Process	Protein catabolic process	IMP	18077552
GO:0045806	Process	Negative regulation of endocytosis	IMP	15256501
GO:0046755	Process	Viral budding	IMP	15256501
GO:0046872	Function	Metal ion binding	IEA
GO:0051865	Process	Protein autoubiquitination	IDA	15256501, 23245322
GO:0061630	Function	Ubiquitin protein ligase activity	IDA	23245322
GO:0061630	Function	Ubiquitin protein ligase activity	IEA
GO:0070086	Process	Ubiquitin-dependent endocytosis	IDA	15256501
GO:1904417	Process	Positive regulation of xenophagy	IMP	23245322
GO:2000786	Process	Positive regulation of autophagosome assembly	IMP	25484098

MIM	HGNC	e!Ensembl
610933	25135	ENSG00000148356

Q6UWE0

Protein name

E3 ubiquitin-protein ligase LRSAM1 (EC 2.3.2.27) (Leucine-rich repeat and sterile alpha motif-containing protein 1) (RING-type E3 ubiquitin transferase LRSAM1) (Tsg101-associated ligase) (hTAL)

Protein function

E3 ubiquitin-protein ligase that mediates monoubiquitination of TSG101 at multiple sites, leading to inactivate the ability of TSG101 to sort endocytic (EGF receptors) and exocytic (HIV-1 viral proteins) cargos (PubMed:15256501). Bacterial recog

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13855	LRR_8	81 → 139	Leucine rich repeat	Repeat
PF13855	LRR_8	127 → 184	Leucine rich repeat	Repeat
PF07647	SAM_2	572 → 630	SAM domain (Sterile alpha motif)	Domain
PF13920	zf-C3HC4_3	671 → 716		Domain

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in adult spinal cord motoneurons as well as in fetal spinal cord and muscle tissue. {ECO:0000269|PubMed:22012984}.

Sequence

MPLFFRKRKPSEEARKRLEYQMCLAKEAGADDILDISKCELSEIPFGAFATCKVLQKKVL
IVHTNHLTSLLPKSCSLLSLATIKVLDLHDNQLTALPDDLGQLTALQVLNVERNQLMQLP
RSIGNLTQLQTLNVKDNKLKELPDTVGELRSLRTLNISGNEIQRLPQMLAHVRTLEMLSL
DASAMVYPPREVCGAGTAAILQFLCKESGLEYYPPSQYLLPILEQDGIENSRDSPDGPTD
RFSREELEWQNRFSDYEKRKEQKMLEKLEFERRLELGQREHTQLLQQSSSQKDEILQTVK
EEQSRLEQGLSEHQRHLNAERQRLQEQLKQTEQNISSRIQKLLQDNQRQKKSSEILKSLE
NERIRMEQLMSITQEETESLRRRDVASAMQQMLTESCKNRLIQMAYESQRQNLVQQACSS
MAEMDERFQQILSWQQMDQNKAISQILQESAMQKAAFEALQVKKDLMHRQIRSQIKLIET
ELLQLTQLELKRKSLDTESLQEMISEQRWALSSLLQQLLKEKQQREEELREILTELEAKS
ETRQENYWLIQYQRLLNQKPLSLKLQEEGMERQLVALLEELSAEHYLPIFAHHRLSLDLL
SQMSPGDLAKVGVSEAGLQHEILRRVQELLDAARIQPELKPPMGEVVTPTAPQEPPESVR
PSAPPAELEVQASECVVCLEREAQMIFLNCGHVCCCQQCCQPLRTCPLCRQDIAQRLRIY
HSS

Sequence length

723

Interactions

View interactions

	Reactome
			Antigen processing: Ubiquitination & Proteasome degradation

890

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Charcot-Marie-Tooth disease	Pathogenic; Likely pathogenic	rs756880678, rs797044913, rs1564287793, rs1588143215, rs1315010600, rs1588143112, rs747130246, rs1835476174, rs1836372698, rs76153575, rs1171946884	RCV000192257 RCV001173632 RCV000789359 RCV000789358 RCV001173629 RCV000857216 RCV001173627 RCV001173631 RCV001173630 RCV001173628 RCV001173633
Charcot-Marie-Tooth disease axonal type 2P	Pathogenic; Likely pathogenic	rs775965001, rs1215220865, rs1156243243, rs752177472, rs1835470775, rs2132110332, rs746159728, rs2132063794, rs961918637, rs2132010730, rs1272943113, rs2132073231, rs2132128455, rs2539396830, rs2539442748 View all (49 more)	RCV001351203 RCV001390983 RCV001386892 RCV001390596 RCV002221182 RCV001782402 RCV001782403 RCV001995161 RCV001956267 RCV002045651 RCV001966683 RCV001992653 RCV002021262 RCV002290054 RCV002290128 RCV002508857 RCV000693004 RCV001224770 RCV002982284 RCV003026775 RCV000696532 RCV000231111 RCV000234917 RCV000258766 RCV003528903 RCV003529240 RCV003529510 RCV003529481 RCV003529634 RCV003529787 RCV003643588 RCV003643878 RCV003643815 RCV003644089 RCV003644094 RCV003644340 RCV003642508 RCV003643362 RCV000468628 RCV000023844 RCV000023845 RCV000551707 RCV000531303 RCV000555275 RCV000034318 RCV000649914 RCV000649917 RCV000649915 RCV000649922 RCV000700711 RCV000700660 RCV000709699 RCV000799835 RCV000792295 RCV000806958 RCV000823842 RCV001205278 RCV001065554 RCV001044043 RCV003642947 RCV002558757 RCV001198443 RCV001216800 RCV001244512 RCV001296574
Charcot-Marie-Tooth disease axonal type 2P-AR	Likely pathogenic; Pathogenic	rs2539464527, rs749012928	RCV006269677 RCV005240490
Familial pancreatic carcinoma	Likely pathogenic	rs76153575	RCV005908894
LRSAM1-related disorder	Pathogenic	rs752177472	RCV004756229
Nonpapillary renal cell carcinoma	Likely pathogenic	rs76153575	RCV005908893
Thyroid cancer, nonmedullary, 1	Pathogenic; Likely pathogenic	rs752177472, rs76153575	RCV005912659 RCV005908895

Show/Hide Unknown Diseases (17)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Likely benign; Benign	rs56131876, rs115106486, rs10987669	RCV005915983 RCV005916259 RCV005905812
Adrenocortical carcinoma, hereditary	Uncertain significance	rs765537196	RCV005931939
Cervical cancer	Likely benign; Benign	rs56131876, rs10987669	RCV005915985 RCV005905814
Charcot-Marie-Tooth disease type 2	Conflicting classifications of pathogenicity; Likely benign; Uncertain significance	rs886063456, rs200242834, rs749626964, rs147734401, rs771510127	RCV000295366 RCV000386689 RCV000337110 RCV000358488 RCV000319125
Charcot-Marie-Tooth disease type 4	Uncertain significance	rs1588144581	RCV000857217
Charcot-Marie-Tooth disease, type I	Uncertain significance	rs1588090984	RCV000857213
Cholangiocarcinoma	Likely benign	rs56131876	RCV005915990
Gastric cancer	Likely benign; Benign	rs56131876, rs150292099, rs10987669	RCV005915987 RCV005900294 RCV005905816
Hepatocellular carcinoma	Conflicting classifications of pathogenicity; Benign	rs201284198, rs2250267	RCV005895390 RCV005902307
Lung cancer	Likely benign	rs56131876	RCV005915991
Malignant tumor of esophagus	Likely benign; Benign	rs56131876, rs116498902, rs10987669	RCV005915984 RCV005900499 RCV005905813
Malignant tumor of urinary bladder	Uncertain significance	rs770711645	RCV005932152
Ovarian serous cystadenocarcinoma	Likely benign	rs115106486	RCV005916260
Sarcoma	Likely benign; Benign	rs56131876, rs10987669	RCV005915986 RCV005905815
Thymoma	Likely benign	rs56131876	RCV005915989
Uterine carcinosarcoma	Likely benign	rs56131876	RCV005915988
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs116498902	RCV005900500

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alcoholic Neuropathy	Associate	30996334
Amyotrophic Lateral Sclerosis	Associate	27615052
Aphasia Broca	Associate	30996334
Charcot Marie Tooth Disease	Associate	20865121, 22012984, 22781092, 24894446, 26556829, 31827005
Charcot Marie Tooth disease X linked recessive 2	Associate	30996334
Colorectal Neoplasms	Stimulate	23045723
Genetic Diseases Inborn	Associate	20865121
Giant Axonal Neuropathy Autosomal Dominant	Associate	22012984
Hereditary Sensory and Autonomic Neuropathies	Associate	24894446
Hirschsprung Disease	Associate	29253842
Neoplasms	Associate	30380781
Nerve Degeneration	Associate	24894446, 27615052
Nervous System Diseases	Associate	24894446, 30996334
Neurodegenerative Diseases	Associate	20865121
Pain	Associate	30996334
Peripheral Nervous System Diseases	Associate	26556829
Polyneuropathies	Associate	22012984, 27615052
Small Cell Lung Carcinoma	Associate	34741430
Stomach Neoplasms	Associate	30380781

LRSAM1 (leucine rich repeat and sterile alpha motif containing 1)