MLANA

melan-A

Basic information

Region (hg38): 9:5890888-5910606

Links

ENSG00000120215 ∙ NCBI:2315 ∙ OMIM:605513 ∙ HGNC:7124 ∙ Uniprot:Q16655 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MLANA 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						0
missense			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in MLANA

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

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

Position	Type	Phenotype	Significance	ClinVar
9-5892542-C-A		not specified	Uncertain significance (Nov 08, 2021)
9-5892542-C-T		not specified	Uncertain significance (Nov 21, 2022)
9-5897618-T-C		not specified	Uncertain significance (Aug 02, 2021)
9-5906947-T-G		not specified	Likely benign (Jun 21, 2022)
9-5906952-A-T		not specified	Uncertain significance (Oct 29, 2021)
9-5908647-A-G		not specified	Uncertain significance (Mar 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MLANA	protein_coding	protein_coding	ENST00000381477	4	19805

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-9	0.0151	125408	8	312	125728	0.00127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.119	67	64.3	1.04	0.00000338	746
Missense in Polyphen		16	17.119	0.93465		193
Synonymous	-0.515	27	23.8	1.13	0.00000132	232
Loss of Function	-1.65	11	6.46	1.70	3.71e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00186	0.00186
Ashkenazi Jewish	0.00	0.00
East Asian	0.0139	0.0136
Finnish	0.00	0.00
European (Non-Finnish)	0.0000723	0.0000703
Middle Eastern	0.0139	0.0136
South Asian	0.000131	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in melanosome biogenesis by ensuring the stability of GPR143. Plays a vital role in the expression, stability, trafficking, and processing of melanocyte protein PMEL, which is critical to the formation of stage II melanosomes. {ECO:0000269|PubMed:15695812, ECO:0000269|PubMed:19717472}.

Recessive Scores

• pRec: 0.376

Intolerance Scores

• loftool: 0.508
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.228
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.641

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Mlana
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype

Gene ontology

• Cellular component: endoplasmic reticulum membrane;Golgi apparatus;trans-Golgi network;integral component of plasma membrane;melanosome
• Molecular function: protein binding