LAMC3 (laminin subunit gamma 3)

Gene

• Entrez ID: 10319
• Gene name: Laminin subunit gamma 3
• Gene symbol: LAMC3
• Synonyms (NCBI Gene): OCCM
• Chromosome: 9
• Chromosome location: 9q34.12
• Summary: Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, n

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs113443891	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs140540789	G>A,T	Conflicting-interpretations-of-pathogenicity, benign-likely-benign	Coding sequence variant, synonymous variant
rs140955110	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, missense variant
rs141497885	C>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant, genic downstream transcript variant
rs141724499	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Genic downstream transcript variant, synonymous variant, coding sequence variant
rs144242690	G>A,C,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs144662546	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic downstream transcript variant, missense variant, coding sequence variant
rs146221263	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant
rs147092908	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign, benign	Genic downstream transcript variant, synonymous variant, missense variant, coding sequence variant
rs149004188	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant
rs192031352	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant
rs199535979	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant
rs201785610	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, genic downstream transcript variant, coding sequence variant
rs387906887	C>T	Pathogenic	Stop gained, coding sequence variant
rs571785750	G>A	Pathogenic	Missense variant, coding sequence variant
rs761516738	TG>-	Pathogenic	Coding sequence variant, inframe indel, stop gained
rs769118642	C>A	Pathogenic	Coding sequence variant, stop gained
rs1057520165	->ACCGCGGGC	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, inframe insertion
rs1426926688	AGCACAG>-	Pathogenic	Coding sequence variant, frameshift variant
rs1554789398	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1554789671	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1564365706	G>A	Pathogenic	Stop gained, coding sequence variant
rs1588171883	C>T	Likely-pathogenic	Stop gained, coding sequence variant, genic downstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1103462	hsa-miR-1	CLIP-seq
MIRT1103463	hsa-miR-1269	CLIP-seq
MIRT1103464	hsa-miR-1269b	CLIP-seq
MIRT1103465	hsa-miR-1288	CLIP-seq
MIRT1103466	hsa-miR-206	CLIP-seq
MIRT1103467	hsa-miR-3138	CLIP-seq
MIRT1103468	hsa-miR-342-3p	CLIP-seq
MIRT1103469	hsa-miR-4515	CLIP-seq
MIRT1103470	hsa-miR-4740-5p	CLIP-seq
MIRT1103471	hsa-miR-4742-3p	CLIP-seq
MIRT1103472	hsa-miR-4800-5p	CLIP-seq
MIRT1103473	hsa-miR-613	CLIP-seq
MIRT1103474	hsa-miR-654-3p	CLIP-seq
MIRT2259415	hsa-miR-3126-3p	CLIP-seq
MIRT2259416	hsa-miR-3162-3p	CLIP-seq
MIRT2259417	hsa-miR-339-5p	CLIP-seq
MIRT2259418	hsa-miR-4663	CLIP-seq
MIRT2259419	hsa-miR-4786-5p	CLIP-seq
MIRT2259420	hsa-miR-769-5p	CLIP-seq
MIRT2390065	hsa-miR-326	CLIP-seq
MIRT2390066	hsa-miR-330-5p	CLIP-seq
MIRT2390067	hsa-miR-4330	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000902	Process	Cell morphogenesis	IEA
GO:0005198	Function	Structural molecule activity	TAS	10225960
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005604	Component	Basement membrane	IEA
GO:0007155	Process	Cell adhesion	IEA
GO:0007601	Process	Visual perception	IEA
GO:0014002	Process	Astrocyte development	IEA
GO:0016020	Component	Membrane	TAS	10225960
GO:0031012	Component	Extracellular matrix	IEA
GO:0031012	Component	Extracellular matrix	TAS	10225960
GO:0060041	Process	Retina development in camera-type eye	IEA

Other IDs

• MIM: 604349
• HGNC: 6494
• e!Ensembl: ENSG00000050555

Protein

• UniProt ID: Q9Y6N6
• Protein name: Laminin subunit gamma-3 (Laminin-12 subunit gamma) (Laminin-14 subunit gamma) (Laminin-15 subunit gamma)
• Protein function: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00055	Laminin_N	35 → 269	Laminin N-terminal (Domain VI)	Family
  PF00053	Laminin_EGF	271 → 324	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	327 → 380	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	383 → 427	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	430 → 477	Laminin EGF domain	Domain
  PF00052	Laminin_B	539 → 671	Laminin B (Domain IV)	Family
  PF00053	Laminin_EGF	669 → 704	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	707 → 752	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	755 → 807	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	810 → 863	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	866 → 914	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	917 → 962	Laminin EGF domain	Domain
  PF00053	Laminin_EGF	965 → 1013	Laminin EGF domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Broadly expressed in: skin, heart, lung, and the reproductive tracts.
• Sequence:

  MAAAALLLGLALLAPRAAGAGMGACYDGAGRPQRCLPVFENAAFGRLAQASHTCGSPPED
  FCPHVGAAGAGAHCQRCDAADPQRHHNASYLTDFHSQDESTWWQSPSMAFGVQYPTSVNI
  TLRLGKAYEITYVRLKFHTSRPESFAIYKRSRADGPWEPYQFYSASCQKTYGRPEGQYLR
  PGEDERVAFCTSEFSDISPLSGGNVAFSTLEGRPSAYNFEESPGLQEWVTSTELLISLDR
  LNTFGDDIFKDPKVLQSYYYAVSDFSVGGRCKCNGHASECGPDVAGQLACRCQHNTTGTD
  CERCLPFFQDRPWARGTAEAAHECLPCNCSGRSEECTFDRELFRSTGHGGRCHHCRDHTA
  GPHCERCQENFYHWDPRMPCQPCDCQSAGSLHLQCDDTGTCACKPTVTGWKCDRCLPGFH
  SLSEGGCRPCTCNPAGSLDTCDPRSGRCPCKENVEGNLCDRCRPGTFNLQPHNPAGCSSC
  FCYGHSKVCASTAQFQVHHILSDFHQGAEGWWARSVGGSEHPPQWSPNGVLLSPEDEEEL
  TAPEKFLGDQRFSYGQPLILTFRVPPGDSPLPVQLRLEGTGLALSLRHSSLSGPQDAGHP
  REVELRFHLQETSEDVAPPLPPFHFQRLLANLTSLRLRVSPGPSPAGPVFLTEVRLTSAR
  PGLSPPASWVEICSCPTGYTGQFCESCAPGYKREMPQGGPYASCVPCTCNQHGTCDPNTG
  ICVCSHHTEGPSCERCLPGFYGNPFAGQADDCQPCPCPGQSACTTIPESREVVCTHCPPG
  QRGRRCEVCDDGFFGDPLGLFGHPQPCHQCQCSGNVDPNAVGNCDPLSGHCLRCLHNTTG
  DHCEHCQEGFYGSALAPRPADKCMPCSCHPQGSVSEQMPCDPVTGQCSCLPHVTARDCSR
  CYPGFFDLQPGRGCRSCKCHPLGSQEDQCHPKTGQCTCRPGVTGQACDRCQLGFFGFSIK
  GCRACRCSPLGAASAQCHENGTCVCRPGFEGYKCDRCHDNFFLTADGTHCQQCPSCYALV
  KEEAAKLKARLTLTEGWLQGSDCGSPWGPLDILLGEAPRGDVYQGHHLLPGAREAFLEQM
  MSLEGAVKAAREQLQRLNKGARCAQAGSQKTCTQLADLEAVLESSEEEILHAAAILASLE
  IPQEGPSQPTKWSHLATEARALARSHRDTATKIAATAWRALLASNTSYALLWNLLEGRVA
  LETQRDLEDRYQEVQAAQKALRTAVAEVLPEAESVLATVQQVGADTAPYLALLASPGALP
  QKSRAEDLGLKAKALEKTVASWQHMATEAARTLQTAAQATLRQTEPLTKLHQEARAALTQ
  ASSSVQAATVTVMGARTLLADLEGMKLQFPRPKDQAALQRKADSVSDRLLADTRKKTKQA
  ERMLGNAAPLSSSAKKKGREAEVLAKDSAKLAKALLRERKQAHRRASRLTSQTQATLQQA
  SQQVLASEARRQELEEAERVGAGLSEMEQQIRESRISLEKDIETLSELLARLGSLDTHQA
  PAQALNETQWALERLRLQLGSPGSLQRKLSLLEQESQQQELQIQGFESDLAEIRADKQNL
  EAILHSLPENCASWQ

• Sequence length: 1575

Pathways

KEGG:

PI3K-Akt signaling pathway
Focal adhesion
ECM-receptor interaction
Toxoplasmosis
Amoebiasis
Human papillomavirus infection
Pathways in cancer
Small cell lung cancer

Reactome:

Laminin interactions
MET activates PTK2 signaling

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
LAMC3-related disorder	Likely pathogenic	rs1833833523	RCV003402880	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Occipital pachygyria and polymicrogyria	Likely pathogenic; Pathogenic	rs781432366, rs2133193948, rs775851709, rs1170064033, rs2133322852, rs1402701697, rs1439284027, rs2538309608, rs2490715564, rs761516738, rs1564365706, rs387906887	RCV001782373 RCV004526873 RCV002492161 RCV002271833 RCV002275673 RCV004587368 RCV003146932 RCV003153290 RCV003990014 RCV000023369 RCV000023370 RCV000023371	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BRAIN DISEASES	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER	—	ClinGen	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONOTRUNCAL HEART MALFORMATIONS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORTICAL MALFORMATIONS, OCCIPITAL	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ENDOMETRIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GENERALIZED ANXIETY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEAD AND NECK MALIGNANT NEOPLASIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Conflicting classifications of pathogenicity; Uncertain significance; Likely benign	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Left ventricular noncompaction	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOUTH NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neonatal death	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ORAL CAVITY CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROPHARYNX CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UPPER AERODIGESTIVE TRACT NEOPLASM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	26394601	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Astrocytoma	Astrocytoma	Pubtator	38307919	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	21572417, 22495309	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorders	Autism Spectrum Disorder	CTD_human_DG	21572417, 28191889		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	Pubtator	34368859	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	36531485	Associate	★☆☆☆☆ Found in Text Mining only
CORTICAL MALFORMATIONS, OCCIPITAL	Cortical Occipital Malformations	UNIPROT_DG	21572413		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORTICAL MALFORMATIONS, OCCIPITAL	Cortical Occipital Malformations	ORPHANET_DG	21572413		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORTICAL MALFORMATIONS, OCCIPITAL	Cortical Occipital Malformations	GENOMICS_ENGLAND_DG	21572413		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORTICAL MALFORMATIONS, OCCIPITAL	Cortical Occipital Malformations	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORTICAL MALFORMATIONS, OCCIPITAL	Cortical Occipital Malformations	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diabetes	Diabetes	BEFREE	24255036		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	24255036		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	24255036	Associate	★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	21572413, 25525159		★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	CTD_human_DG	21572413		★☆☆☆☆ Found in Text Mining only
Endometriosis	Endometriosis	GWASCAT_DG	28333195		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Endometriosis	Endometriosis	Pubtator	36232817	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Epilepsy	Epilepsy	Pubtator	26802095	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	29247375		★☆☆☆☆ Found in Text Mining only
Lip and Oral Cavity Carcinoma	Lip and Oral Cavity Carcinoma	BEFREE	27749845		★☆☆☆☆ Found in Text Mining only
Lissencephaly	Lissencephaly	Pubtator	33639934	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of anterior portion of floor of mouth	Malignant Neoplasm Of Anterior Portion Of Floor Of Mouth	GWASCAT_DG	27749845		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of floor of mouth	Malignant neoplasm of floor of mouth	GWASCAT_DG	27749845		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lateral floor of mouth	Malignant tumor of lateral floor of mouth	GWASCAT_DG	27749845		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of mouth	Malignant neoplasm of mouth	BEFREE	27749845		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of mouth	Malignant neoplasm of mouth	CTD_human_DG	27749845		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of mouth	Malignant neoplasm of mouth	GWASCAT_DG	27749845		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of other sites within the lip and oral cavity	Malignant Neoplasm Of Lip And Oral Cavity	GWASCAT_DG	27749845		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of other specified parts of mouth	Malignant Neoplasm Of Mouth	GWASCAT_DG	27749845		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	30426560		★☆☆☆☆ Found in Text Mining only
Mouth Neoplasms	Mouth Neoplasms	CTD_human_DG	27749845		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mouth Neoplasms	Mouth neoplasm	Pubtator	27749845	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Occipital pachygyria and polymicrogyria	Occipital Pachygyria And Polymicrogyria	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pachygyria	Pachygyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Periventricular Nodular Heterotopia	Periventricular nodular heterotopia	Pubtator	33639934	Associate	★☆☆☆☆ Found in Text Mining only
Pharyngeal Neoplasms	Pharyngeal Neoplasms	GWASCAT_DG	27749845		★☆☆☆☆ Found in Text Mining only
Pituitary Neoplasms	Pituitary neoplasm	Pubtator	36686480	Associate	★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	BEFREE	29247375		★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	Pubtator	33639934	Associate	★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	26802095	Associate	★☆☆☆☆ Found in Text Mining only