LRMDA (leucine rich melanocyte differentiation associated)

Gene

• Entrez ID: 83938
• Gene name: Leucine rich melanocyte differentiation associated
• Gene symbol: LRMDA
• Synonyms (NCBI Gene): C10orf11, CDA017
• Chromosome: 10
• Chromosome location: 10q22.2-q22.3
• Summary: This gene encodes a leucine-rich repeat protein. The encoded protein is thought to play a role in melanocyte differentiation. Mutations in this gene have been associated with autosomal recessive oculocutaneous albinism 7 (OCA7). Alternatively spliced tran

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs146123023	C>-	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, intron variant, frameshift variant
rs147768808	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, non coding transcript variant, synonymous variant
rs587776952	C>T	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs587776953	->C	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs878854351	C>A,T	Likely-pathogenic	Synonymous variant, non coding transcript variant, coding sequence variant, missense variant
rs886043155	C>A,T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant, synonymous variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0030154	Process	Cell differentiation	IEA
GO:0030318	Process	Melanocyte differentiation	IBA
GO:0030318	Process	Melanocyte differentiation	IMP	23395477

Other IDs

• MIM: 614537
• HGNC: 23405
• e!Ensembl: ENSG00000148655

Protein

• UniProt ID: Q9H2I8
• Protein name: Leucine-rich melanocyte differentiation-associated protein
• Protein function: Required for melanocyte differentiation.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF14580	LRR_9	5 → 150		Repeat

• Tissue specificity: TISSUE SPECIFICITY: In the embryo, expressed in melanoblasts. In the fetus, expressed in melanocytes. Not detected in retinal pigment epithelial cells. {ECO:0000269|PubMed:23395477}.
• Sequence:

  MEKYLSLSGNHSSNKRSLEGLSAFRSLEELILDNNQLGDDLVLPGLPRLHTLTLNKNRIT
  DLENLLDHLAEVTPALEYLSLLGNVACPNELVSLEKDEEDYKRYRCFVLYKLPNLKFLDA
  QKVTRQEREEALVRGVFMKVVKPKASSEDVASSPERHYTPLPSASRELTSHQGVLGKCRY
  VYYGKNSEGNRFIRDDQL

• Sequence length: 198

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
LRMDA-related disorder	Pathogenic	rs587776953	RCV003974869	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Oculocutaneous albinism type 7	Likely pathogenic; Pathogenic	rs878854351, rs587776952, rs587776953	RCV000234797 RCV000034833 RCV000034834	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANOREXIA NERVOSA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	CTD, Disgenet, GWAS catalog CTD, Disgenet, GWAS catalog CTD, Disgenet, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FLUTTER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIAC ARRHYTHMIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIOEMBOLIC STROKE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EATING DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEPHROLITHIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR SARCOIDOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPEN-ANGLE GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, HIP	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, KNEE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOSARCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POST-TRAUMATIC STRESS DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RESTLESS LEGS SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
THYROTOXIC PERIODIC PARALYSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Albinism	Albinism	BEFREE	23395477		★☆☆☆☆ Found in Text Mining only
Albinism	Albinism	Pubtator	35488210	Associate	★☆☆☆☆ Found in Text Mining only
Albinism	Albinism	HPO_DG			★☆☆☆☆ Found in Text Mining only
ALBINISM, OCULOCUTANEOUS, TYPE VII	Oculocutaneous albinism	GENOMICS_ENGLAND_DG	23395477		★☆☆☆☆ Found in Text Mining only
ALBINISM, OCULOCUTANEOUS, TYPE VII	Oculocutaneous albinism	ORPHANET_DG	23395477		★☆☆☆☆ Found in Text Mining only
ALBINISM, OCULOCUTANEOUS, TYPE VII	Oculocutaneous albinism	CLINVAR_DG	26818737		★☆☆☆☆ Found in Text Mining only
ALBINISM, OCULOCUTANEOUS, TYPE VII	Oculocutaneous albinism	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Alopecia	Alopecia	GWASCAT_DG	28196072		★☆☆☆☆ Found in Text Mining only
Alopecia, Androgenetic, 1	Androgenetic Alopecia	GWASCAT_DG	27182965, 29146897		★☆☆☆☆ Found in Text Mining only
Alopecia, Androgenetic, 2	Androgenetic Alopecia	GWASCAT_DG	27182965, 29146897		★☆☆☆☆ Found in Text Mining only
Alopecia, Androgenetic, 3	Androgenetic Alopecia	GWASCAT_DG	27182965, 29146897		★☆☆☆☆ Found in Text Mining only
Alopecia, Male Pattern	Alopecia, Male Pattern	GWASCAT_DG	27182965, 29146897		★☆☆☆☆ Found in Text Mining only
Androgenetic Alopecia	Androgenetic Alopecia	GWASCAT_DG	27182965, 29146897		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Atrial Fibrillation	Atrial Fibrillation	GWASCAT_DG	29892015, 30061737		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Atrial Fibrillation	Atrial Fibrillation	CTD_human_DG	29892015, 30061737		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Carcinoma	Breast Carcinoma	BEFREE	22180457		★☆☆☆☆ Found in Text Mining only
Chronic Obstructive Airway Disease	Chronic Obstructive Pulmonary Disease	GWASCAT_DG	30804561		★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	19844253	Associate	★☆☆☆☆ Found in Text Mining only
Congenital chromosomal disease	Congenital Chromosomal Disease	BEFREE	19844253		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	36104811	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	GWASCAT_DG	30718926		★☆☆☆☆ Found in Text Mining only
Disorder of eye	Disorder Of Eye	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	27031267		★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	19844253		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	22180457		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ocular albinism, type I	Ocular albinism	BEFREE	30679655		★☆☆☆☆ Found in Text Mining only
Oculocutaneous albinism type 7	Oculocutaneous albinism	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Paroxysmal atrial fibrillation	Paroxysmal atrial fibrillation	CTD_human_DG	29892015, 30061737		★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	GWASDB_DG	23740937		★☆☆☆☆ Found in Text Mining only
Uranostaphyloschisis	Uranostaphyloschisis	BEFREE	27031267		★☆☆☆☆ Found in Text Mining only