LAMA3 (Laminin subunit alpha-3) variants and mutations
LAMA3 (also known as Laminin subunit alpha-3) is a human protein-coding gene encoding a laminin subunit alpha-3 protein. It contributes to laminin-332 in epithelial basement membranes, where it supports stable attachment of basal keratinocytes to underlying matrix. Biallelic pathogenic variants can cause junctional epidermolysis bullosa, while some variants cause amelogenesis imperfecta or milder skin disease. This analysis covers 4,223 LAMA3 variants and mutations. Of these, 75% have computational variant effect predictions. Disease context includes laryngo-onycho-cutaneous syndrome, Junctional epidermolysis bullosa, Herlitz type, and junctional epidermolysis bullosa Herlitz type. Example LAMA3 variants include A2T, A2P, and A2S.
Variant analysis overview
- Gene: LAMA3
- Protein: Laminin subunit alpha-3
- UniProt accession: Q16787
- Organism: Homo sapiens
- Variants analyzed: 4223
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 3,834 unspecified-consequence records; 262 missense variants; 91 synonymous variants; 22 frameshift variants; 3 in-frame deletions; 9 stop-gained variants; 1 splice acceptor variant; 1 splice-region variants; 1 in-frame insertions
- Prediction scores: 3,152 variants have prediction scores (75% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: laryngo-onycho-cutaneous syndrome, Junctional epidermolysis bullosa, Herlitz type, junctional epidermolysis bullosa Herlitz type, LOC syndrome, epidermolysis bullosa, junctional 2B, severe, junctional epidermolysis bullosa, non-Herlitz type, epidermolysis bullosa, junctional 2A, intermediate, junctional epidermolysis bullosa, Generalized junctional epidermolysis bullosa, non-Herlitz type, generalized junctional epidermolysis bullosa non-Herlitz type, epidermolysis bullosa, junctional 4, intermediate, eye disorder.
Protein structure and variant hotspots
- Protein features: 22 domains; 5 post-translational modification sites.
- Structural context: 2,479 variants have structural context.
- PTM context: 10 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable LAMA3 variants
Examples include A2T, A2P, A2S, A2G, A2E, A2V, A2A, A3S. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- A2T (p.Ala2Thr), gnomAD 18-23689687-G-A, REVEL 0.06, CADD 22.80
- A2P (p.Ala2Pro), gnomAD 18-23689687-G-C, REVEL 0.08, CADD 24.20
- A2S (p.Ala2Ser), gnomAD 18-23689687-G-T, REVEL 0.07, CADD 22.30
- A2G (p.Ala2Gly), gnomAD 18-23689688-C-G, REVEL 0.03, CADD 20.50
- A2E (p.Ala2Glu), gnomAD 18-23689688-C-A, REVEL 0.02, CADD 22.40
- A2V (p.Ala2Val), gnomAD 18-23689688-C-T, REVEL 0.04, CADD 20.50
- A2A (p.Ala2Ala), gnomAD 18-23689689-G-A, CADD 13.20
- A3S (p.Ala3Ser), TOPMed rs2060540604, REVEL 0.01, CADD 17.30
- A3V (p.Ala3Val), Ensembl rs2145782285, REVEL 0.01, CADD 18.40
- A3T (p.Ala3Thr), gnomAD 18-23689690-G-A, REVEL 0.01, CADD 17.70
- A3E (p.Ala3Glu), gnomAD 18-23689691-C-A, REVEL 0.02, CADD 21.60
- A3A (p.Ala3Ala), gnomAD 18-23689692-G-T, CADD 11.30
- A4D (p.Ala4Asp), TOPMed rs1372314794, gnomAD rs1372314794, REVEL 0.03, CADD 17.00
- A4G (p.Ala4Gly), TOPMed rs1372314794, gnomAD rs1372314794, REVEL 0.04, CADD 13.80
- A4P (p.Ala4Pro), Ensembl rs1004550988
- A4V (p.Ala4Val), TOPMed rs1372314794, gnomAD rs1372314794, REVEL 0.05, CADD 16.90
- A4T (p.Ala4Thr), gnomAD 18-23689693-G-A, REVEL 0.05, CADD 22.90
- A4S (p.Ala4Ser), gnomAD 18-23689693-G-T, REVEL 0.05, CADD 20.00
- A4A (p.Ala4Ala), rs943822767, gnomAD 18-23689695-C-T, CADD 9.65
- A5E (p.Ala5Glu), TOPMed rs2060541050, gnomAD rs2060541050, REVEL 0.01, CADD 5.94, Uncertain significance, Inborn genetic diseases
- A5S (p.Ala5Ser), TOPMed rs1568076555, gnomAD rs1568076555, REVEL 0.01, CADD 2.92
- A5T (p.Ala5Thr), gnomAD 18-23689696-G-A, REVEL 0.01, CADD 5.20
- A5P (p.Ala5Pro), gnomAD 18-23689696-G-C, REVEL 0.01, CADD 7.69
- A5V (p.Ala5Val), gnomAD 18-23689697-C-T, REVEL 0.00, CADD 8.89
- A5A (p.Ala5Ala), rs2060541111, gnomAD 18-23689698-G-A, CADD 10.00
- R6G (p.Arg6Gly), TOPMed rs899550243, gnomAD rs899550243, REVEL 0.03, CADD 13.90
- R6P (p.Arg6Pro), Ensembl rs2145782450
- R6W (p.Arg6Trp), TOPMed rs899550243, gnomAD rs899550243, REVEL 0.11, CADD 21.80
- R6R (p.Arg6Arg), gnomAD 18-23689699-C-A, CADD 9.39
- R6Q (p.Arg6Gln), gnomAD 18-23689700-G-A, REVEL 0.05, CADD 16.50
- P7L (p.Pro7Leu), rs1555670401, gnomAD 18-23689699-CG-C, CADD 22.60
- P7A (p.Pro7Ala), gnomAD 18-23689702-C-G, REVEL 0.04, CADD 5.02
- P7S (p.Pro7Ser), gnomAD 18-23689702-C-T, REVEL 0.03, CADD 10.60
- P7T (p.Pro7Thr), gnomAD 18-23689702-C-A, REVEL 0.03, CADD 8.83
- P7H (p.Pro7His), gnomAD 18-23689703-C-A, REVEL 0.03, CADD 15.50
- P7P (p.Pro7Pro), gnomAD 18-23689704-T-C, CADD 10.60
- R8P (p.Arg8Pro), TOPMed rs1217483724, gnomAD rs1217483724
- R8Q (p.Arg8Gln), TOPMed rs1217483724, gnomAD rs1217483724, REVEL 0.01, CADD 4.58
- R8W (p.Arg8Trp), TOPMed rs1000956325, REVEL 0.03, CADD 22.40
- R8R (p.Arg8Arg), gnomAD 18-23689705-C-A, CADD 11.80
- R8G (p.Arg8Gly), gnomAD 18-23689705-C-G, REVEL 0.02, CADD 15.60
- R8L (p.Arg8Leu), gnomAD 18-23689706-G-T, REVEL 0.01, CADD 5.59
- G9D (p.Gly9Asp), gnomAD rs1197054682, REVEL 0.02, CADD 17.70, Uncertain significance, Inborn genetic diseases
- G9S (p.Gly9Ser), gnomAD 18-23689708-G-A, REVEL 0.03, CADD 16.30
- G9C (p.Gly9Cys), gnomAD 18-23689708-G-T, REVEL 0.07, CADD 23.30
- G9V (p.Gly9Val), gnomAD 18-23689709-G-T, REVEL 0.05, CADD 17.60
- G9G (p.Gly9Gly), gnomAD 18-23689710-T-C, CADD 12.40
- R10P (p.Arg10Pro), TOPMed rs1014633904, gnomAD rs1014633904, REVEL 0.05, CADD 22.70
- R10Q (p.Arg10Gln), TOPMed rs1014633904, gnomAD rs1014633904, REVEL 0.07, CADD 19.10
- R10W (p.Arg10Trp), TOPMed rs2060541573, REVEL 0.02, CADD 5.24
- R10R (p.Arg10Arg), gnomAD 18-23689711-C-A, CADD 5.38
- R10G (p.Arg10Gly), gnomAD 18-23689711-C-G, REVEL 0.01, CADD 1.51
- R10L (p.Arg10Leu), gnomAD 18-23689712-G-T, REVEL 0.07, CADD 16.20
- A11P (p.Ala11Pro), TOPMed rs1053428428, gnomAD rs1053428428
- A11T (p.Ala11Thr), TOPMed rs1053428428, gnomAD rs1053428428, REVEL 0.01, CADD 10.90
- A11G (p.Ala11Gly), gnomAD 18-23689715-C-G, REVEL 0.01, CADD 10.80
- A11E (p.Ala11Glu), gnomAD 18-23689715-C-A, REVEL 0.04, CADD 16.20
- A11V (p.Ala11Val), gnomAD 18-23689715-C-T, REVEL 0.01, CADD 12.70
- L12Q (p.Leu12Gln), ExAC rs769479220, gnomAD rs769479220, REVEL 0.02, CADD 5.70
- L12V (p.Leu12Val), Ensembl rs2060541809, REVEL 0.01, CADD 6.42
- L12R (p.Leu12Arg), gnomAD 18-23689717-CT-C, CADD 13.00
- L12M (p.Leu12Met), gnomAD 18-23689717-C-A, REVEL 0.01, CADD 9.62
- L12L (p.Leu12Leu), rs2060541809, gnomAD 18-23689717-C-T, CADD 8.04
- L12P (p.Leu12Pro), gnomAD 18-23689718-T-C, REVEL 0.02, CADD 6.77
- G13E (p.Gly13Glu), TOPMed rs1157533708, gnomAD rs1157533708, REVEL 0.02, CADD 8.14
- G13R (p.Gly13Arg), gnomAD rs1309244363, REVEL 0.02, CADD 4.52
- G13V (p.Gly13Val), TOPMed rs1157533708, gnomAD rs1157533708, REVEL 0.02, CADD 9.81, Uncertain significance, Inborn genetic diseases; not provided
- G13W (p.Gly13Trp), gnomAD 18-23689720-G-T, REVEL 0.09, CADD 18.70
- G13G (p.Gly13Gly), rs1207926328, gnomAD 18-23689722-G-T, CADD 8.50
- P14Q (p.Pro14Gln), gnomAD 18-23689718-TG-T, CADD 16.70
- P14S (p.Pro14Ser), gnomAD 18-23689723-C-T, REVEL 0.01, CADD 4.39
- P14T (p.Pro14Thr), gnomAD 18-23689723-C-A, REVEL 0.01, CADD 2.63
- P14L (p.Pro14Leu), gnomAD 18-23689724-C-T, REVEL 0.01, CADD 11.00
- P14P (p.Pro14Pro), gnomAD 18-23689725-A-G, CADD 4.69
- V15A (p.Val15Ala), gnomAD rs1255233442, REVEL 0.02, CADD 10.70
- V15L (p.Val15Leu), gnomAD 18-23689726-G-C, REVEL 0.00, CADD 1.45
- V15I (p.Val15Ile), gnomAD 18-23689726-G-A, REVEL 0.01, CADD 1.91
- V15V (p.Val15Val), rs775332554, gnomAD 18-23689728-A-G, CADD 5.49
- L16M (p.Leu16Met), gnomAD 18-23689729-C-A, REVEL 0.06, CADD 14.10
- L16L (p.Leu16Leu), gnomAD 18-23689729-C-T, CADD 8.84
- P17S (p.Pro17Ser), gnomAD 18-23689732-C-T, REVEL 0.01, CADD 9.03
- P17T (p.Pro17Thr), gnomAD 18-23689732-C-A, REVEL 0.02, CADD 8.64
- P17Q (p.Pro17Gln), gnomAD 18-23689733-C-A, REVEL 0.05, CADD 0.83
- P17L (p.Pro17Leu), gnomAD 18-23689733-C-T, REVEL 0.01, CADD 0.25
- P17R (p.Pro17Arg), gnomAD 18-23689733-C-G, REVEL 0.06, CADD 0.84
- P17P (p.Pro17Pro), gnomAD 18-23689734-G-T, CADD 7.78
- P18A (p.Pro18Ala), TOPMed rs1009802661, gnomAD rs1009802661, REVEL 0.07, CADD 8.17
- P18Q (p.Pro18Gln), 1000Genomes rs748928607, ExAC rs748928607, TOPMed rs748928607, gnomAD rs748928607, REVEL 0.04, CADD 13.80, Uncertain significance
- P18R (p.Pro18Arg), 1000Genomes rs748928607, ExAC rs748928607, TOPMed rs748928607, gnomAD rs748928607, REVEL 0.03, CADD 13.80, Uncertain significance, Inborn genetic diseases
- P18T (p.Pro18Thr), gnomAD 18-23689735-C-A, REVEL 0.06, CADD 14.30
- P18S (p.Pro18Ser), gnomAD 18-23689735-C-T, REVEL 0.04, CADD 13.40
- P18L (p.Pro18Leu), gnomAD 18-23689736-C-T, REVEL 0.03, CADD 13.60
- P18P (p.Pro18Pro), gnomAD 18-23689737-G-T, CADD 9.17
- T19M (p.Thr19Met), gnomAD 18-23689739-C-T, REVEL 0.07, CADD 17.20
- T19R (p.Thr19Arg), gnomAD 18-23689739-C-G, REVEL 0.08, CADD 15.20
- T19T (p.Thr19Thr), gnomAD 18-23689740-G-A, CADD 7.72
- P20Q (p.Pro20Gln), TOPMed rs2060542611, gnomAD rs2060542611, REVEL 0.01, CADD 5.08
- P20G (p.Pro20Gly), gnomAD 18-23689738-ACGCC, CADD 23.00
- P20S (p.Pro20Ser), gnomAD 18-23689741-C-T, REVEL 0.03, CADD 4.73
- P20T (p.Pro20Thr), gnomAD 18-23689741-C-A, REVEL 0.04, CADD 4.49
- P20R (p.Pro20Arg), gnomAD 18-23689742-C-G, REVEL 0.02, CADD 3.80
- P20L (p.Pro20Leu), gnomAD 18-23689742-C-T, REVEL 0.02, CADD 4.50
- P20P (p.Pro20Pro), gnomAD 18-23689743-G-T, CADD 8.47
- L21M (p.Leu21Met), gnomAD 18-23689744-C-A, REVEL 0.05, CADD 14.00
- L21L (p.Leu21Leu), gnomAD 18-23689744-C-T, CADD 9.03
- L21P (p.Leu21Pro), gnomAD 18-23689745-T-C, REVEL 0.13, CADD 21.90
- L21Q (p.Leu21Gln), gnomAD 18-23689745-T-A, REVEL 0.19, CADD 21.80
- L22F (p.Leu22Phe), Ensembl rs2060542743, REVEL 0.04, CADD 15.40
- L22P (p.Leu22Pro), Ensembl rs1027667940, REVEL 0.13, CADD 18.40
- L22I (p.Leu22Ile), gnomAD 18-23689747-C-A, REVEL 0.03, CADD 18.80
- L22L (p.Leu22Leu), gnomAD 18-23689749-C-A, CADD 4.99
- L23L (p.Leu23Leu), rs1413334163, gnomAD 18-23689750-C-T, CADD 7.92
- L23M (p.Leu23Met), gnomAD 18-23689750-C-A, REVEL 0.07, CADD 15.20
- L23P (p.Leu23Pro), gnomAD 18-23689751-T-C, REVEL 0.08, CADD 13.80
- L24M (p.Leu24Met), gnomAD 18-23689753-C-A, REVEL 0.08, CADD 17.60
- L24L (p.Leu24Leu), gnomAD 18-23689753-C-T, CADD 8.76
- L24P (p.Leu24Pro), gnomAD 18-23689754-T-C, REVEL 0.18, CADD 13.40
- V25A (p.Val25Ala), ExAC rs768021480, gnomAD rs768021480, REVEL 0.01, CADD 3.00
- V25L (p.Val25Leu), TOPMed rs1033783069, gnomAD rs1033783069, REVEL 0.02, CADD 0.05
- V25I (p.Val25Ile), gnomAD 18-23689756-G-A, REVEL 0.01, CADD 0.13
- V25E (p.Val25Glu), gnomAD 18-23689757-T-A, REVEL 0.09, CADD 5.46
- V25V (p.Val25Val), gnomAD 18-23689758-A-G, CADD 8.53
- L26M (p.Leu26Met), gnomAD 18-23689759-C-A, REVEL 0.03, CADD 13.60
- L26L (p.Leu26Leu), gnomAD 18-23689759-C-T, CADD 8.70
- L26P (p.Leu26Pro), gnomAD 18-23689760-T-C, REVEL 0.11, CADD 16.70
- R27L (p.Arg27Leu), TOPMed rs1337980671, gnomAD rs1337980671, REVEL 0.01, CADD 0.55
- R27P (p.Arg27Pro), TOPMed rs1337980671, gnomAD rs1337980671, REVEL 0.03, CADD 3.02
- R27Q (p.Arg27Gln), TOPMed rs1337980671, gnomAD rs1337980671, REVEL 0.01, CADD 1.53
- R27W (p.Arg27Trp), gnomAD 18-23689762-C-T, REVEL 0.08, CADD 14.00
- R27R (p.Arg27Arg), rs371129898, gnomAD 18-23689762-C-A, CADD 7.45
- V28M (p.Val28Met), rs761308269, ClinGen CA8914176, ClinVar RCV002694627, ClinVar RCV004538880, REVEL 0.01, CADD 2.25, Uncertain significance, Inborn genetic diseases; LAMA3-related disorder
- V28L (p.Val28Leu), gnomAD 18-23689765-G-T, REVEL 0.00, CADD 0.08
- V28A (p.Val28Ala), gnomAD 18-23689766-T-C, REVEL 0.02, CADD 5.87
- V28V (p.Val28Val), gnomAD 18-23689767-G-T, CADD 8.98
- L29L (p.Leu29Leu), gnomAD 18-23689768-C-T, CADD 6.99
- L29M (p.Leu29Met), gnomAD 18-23689768-C-A, REVEL 0.06, CADD 14.60
- L29P (p.Leu29Pro), gnomAD 18-23689769-T-C, REVEL 0.08, CADD 15.90
- L29Q (p.Leu29Gln), gnomAD 18-23689769-T-A, REVEL 0.17, CADD 19.60
- P30T (p.Pro30Thr), TOPMed rs1407288295, gnomAD rs1407288295, REVEL 0.01, CADD 15.00
- P30S (p.Pro30Ser), gnomAD 18-23689771-C-T, REVEL 0.02, CADD 15.90
- P30A (p.Pro30Ala), gnomAD 18-23689771-C-G, REVEL 0.02, CADD 12.80
- P30Q (p.Pro30Gln), gnomAD 18-23689772-C-A, REVEL 0.01, CADD 12.00
- P30L (p.Pro30Leu), gnomAD 18-23689772-C-T, REVEL 0.02, CADD 13.40
- P30P (p.Pro30Pro), gnomAD 18-23689773-A-G, CADD 4.74
- A31T (p.Ala31Thr), TOPMed rs2060543472, gnomAD rs2060543472, REVEL 0.01, CADD 16.00
- A31S (p.Ala31Ser), gnomAD 18-23689774-G-T, REVEL 0.01, CADD 12.30
- A31V (p.Ala31Val), gnomAD 18-23689775-C-T, REVEL 0.00, CADD 13.60
- A31D (p.Ala31Asp), gnomAD 18-23689775-C-A, REVEL 0.03, CADD 14.60
- A31A (p.Ala31Ala), gnomAD 18-23689776-C-A, CADD 6.68
- C32G (p.Cys32Gly), TOPMed rs2060543586, REVEL 0.02, CADD 8.38
- C32S (p.Cys32Ser), gnomAD 18-23689777-TG-T, CADD 17.40
- C32R (p.Cys32Arg), gnomAD 18-23689777-T-C, REVEL 0.08, CADD 9.45
- C32F (p.Cys32Phe), gnomAD 18-23689778-G-T, REVEL 0.04, CADD 4.84
- C32Y (p.Cys32Tyr), gnomAD 18-23689778-G-A, REVEL 0.03, CADD 2.18
- C32C (p.Cys32Cys), gnomAD 18-23689779-C-T, CADD 7.63
- C32* (p.Cys32Ter), gnomAD 18-23689779-C-A, CADD 32.00
- G33R (p.Gly33Arg), rs1363412150, ClinGen CA402233200, ClinVar RCV003184811, gnomAD rs1363412150, REVEL 0.02, CADD 7.51, Uncertain significance, Inborn genetic diseases
- G33W (p.Gly33Trp), gnomAD 18-23689780-G-T, REVEL 0.12, CADD 15.50
- G33E (p.Gly33Glu), gnomAD 18-23689781-G-A, REVEL 0.10, CADD 14.00
- G33V (p.Gly33Val), gnomAD 18-23689781-G-T, REVEL 0.09, CADD 13.80
- G33G (p.Gly33Gly), gnomAD 18-23689782-G-T, CADD 6.00
- p.Ala34 Gly67del, gnomAD 18-23689774-GCCTG, CADD 22.00
- A34R (p.Ala34Arg), gnomAD 18-23689779-CG-C, CADD 9.40
- A34P (p.Ala34Pro), gnomAD 18-23689783-G-C, REVEL 0.02, CADD 15.40
- A34S (p.Ala34Ser), gnomAD 18-23689783-G-T, REVEL 0.02, CADD 4.12
- A34T (p.Ala34Thr), gnomAD 18-23689783-G-A, REVEL 0.02, CADD 7.67
- A34E (p.Ala34Glu), gnomAD 18-23689784-C-A, REVEL 0.07, CADD 13.20
- A34V (p.Ala34Val), gnomAD 18-23689784-C-T, REVEL 0.01, CADD 10.10
- A34A (p.Ala34Ala), gnomAD 18-23689785-G-C, CADD 6.98
- T35I (p.Thr35Ile), TOPMed rs919247921, gnomAD rs919247921, REVEL 0.01, CADD 10.10
- T35A (p.Thr35Ala), gnomAD 18-23689786-A-G, REVEL 0.01, CADD 2.01
- T35S (p.Thr35Ser), gnomAD 18-23689786-A-T, REVEL 0.00, CADD 3.00
- T35N (p.Thr35Asn), gnomAD 18-23689787-C-A, REVEL 0.02, CADD 8.56
- T35T (p.Thr35Thr), gnomAD 18-23689788-C-T, CADD 6.25
- A36S (p.Ala36Ser), NCI-TCGA Cosmic COSV1005, cosmic curated COSV10055, REVEL 0.02, CADD 22.40, Variant assessed as somatic; moderate impact.
- A36T (p.Ala36Thr), gnomAD 18-23689789-G-A, REVEL 0.02, CADD 24.00
- A36D (p.Ala36Asp), gnomAD 18-23689790-C-A, REVEL 0.03, CADD 23.30
- A36V (p.Ala36Val), gnomAD 18-23689790-C-T, REVEL 0.03, CADD 20.70
- A36A (p.Ala36Ala), gnomAD 18-23689791-T-C, CADD 9.00
- R37Q (p.Arg37Gln), TOPMed rs1276923266, gnomAD rs1276923266, REVEL 0.03, CADD 9.45
Public LAMA3 analysis runs
- LAMA3 analysis run — LAMA3 (4,223 variants) — completed 2026-08-22