LRMDA

leucine rich melanocyte differentiation associated, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 10:75431624-76560168

Previous symbols: [ "C10orf11" ]

Links

ENSG00000148655 ∙ NCBI:83938 ∙ OMIM:614537 ∙ HGNC:23405 ∙ Uniprot:Q9H2I8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• oculocutaneous albinism type 7 (Supportive), mode of inheritance: AR
• oculocutaneous albinism type 7 (Strong), mode of inheritance: AR
• oculocutaneous albinism type 7 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Albinism, oculocutaneous, type VII	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic; Ophthalmologic	23395477

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRMDA gene.

• not provided (5 variants)
• LRMDA-related disorder (1 variants)
• Oculocutaneous albinism type 7 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRMDA gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				28	4	32
missense		1	31	2	4	38
nonsense	2	1				3
start loss						0
frameshift	3					3
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region			3	3		6
non coding				16	2	18
Total	5	4	31	46	10

Highest pathogenic variant AF is 0.000191

Variants in LRMDA

This is a list of pathogenic ClinVar variants found in the LRMDA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-75438487-C-T		LRMDA-related disorder	Benign (Jun 18, 2019)
10-75782986-A-G			Uncertain significance (Oct 13, 2022)
10-75782995-TC-T		not specified	Conflicting classifications of pathogenicity (Jan 29, 2024)
10-75782999-C-T			Benign (Nov 07, 2023)
10-75783000-G-A			Uncertain significance (Jul 20, 2022)
10-75783007-A-C			Likely benign (Nov 19, 2023)
10-75783039-C-T			Likely benign (Oct 29, 2021)
10-76036025-G-GC		Oculocutaneous albinism type 7 • LRMDA-related disorder	Pathogenic (Jan 18, 2024)
10-76036030-T-A			Uncertain significance (Apr 30, 2022)
10-76036034-G-C			Uncertain significance (Jul 30, 2022)
10-76036035-G-A			Likely benign (Jan 12, 2024)
10-76036054-T-C			Likely benign (Sep 24, 2022)
10-76036067-A-C			Uncertain significance (Jun 01, 2022)
10-76036069-C-T		not specified • Oculocutaneous albinism type 7	Conflicting classifications of pathogenicity (Jan 25, 2024)
10-76036082-T-G			Uncertain significance (Apr 12, 2022)
10-76036084-G-A			Uncertain significance (Aug 24, 2022)
10-76036092-A-G			Likely benign (Jun 24, 2022)
10-76036098-A-G			Benign (Jan 09, 2024)
10-76036104-A-G		not specified	Benign (Jan 29, 2024)
10-76036105-C-G		Inborn genetic diseases	Uncertain significance (Apr 01, 2022)
10-76036107-G-A			Likely benign (Oct 16, 2023)
10-76036112-C-T			Uncertain significance (Aug 22, 2022)
10-76036113-C-T			Likely benign (Sep 09, 2023)
10-76036125-C-A			Uncertain significance (Mar 14, 2022)
10-76036128-G-A			Likely benign (Sep 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRMDA	protein_coding	protein_coding	ENST00000372499	6	958928

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000259	0.789	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.115	112	109	1.03	0.00000584	1271
Missense in Polyphen		31	29.613	1.0468		399
Synonymous	-0.792	55	48.0	1.15	0.00000291	381
Loss of Function	1.11	7	11.0	0.638	6.09e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000202	0.000202
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000211	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000664	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for melanocyte differentiation. {ECO:0000269|PubMed:23395477}.
• Disease: DISEASE: Albinism, oculocutaneous, 7 (OCA7) [MIM:615179]: A disorder of pigmentation characterized by reduced biosynthesis of melanin in the skin, hair and eyes. Patients show reduced or lacking pigmentation associated with classic albinism ocular abnormalities, including decreased visual acuity, macular hypoplasia, optic dysplasia, atypical choroidal vessels, and nystagmus. {ECO:0000269|PubMed:23395477}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0845

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• pHI: 0.0968
• hipred: N
• hipred_score: 0.290
• ghis: 0.389

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Lrmda
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype; immune system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: lrmda
• Affected structure: melanocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: melanocyte differentiation