MAL

mal, T cell differentiation protein, the group of MARVEL domain containing

Basic information

Region (hg38): 2:95025677-95053992

Links

ENSG00000172005 ∙ NCBI:4118 ∙ OMIM:188860 ∙ HGNC:6817 ∙ Uniprot:P21145 ∙ 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 MAL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAL 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in MAL

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

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

Position	Type	Phenotype	Significance	ClinVar
2-95025820-A-G		not specified	Uncertain significance (Jan 23, 2024)
2-95025832-A-G		not specified	Uncertain significance (Nov 07, 2023)
2-95025832-A-T		not specified	Uncertain significance (May 31, 2024)
2-95025854-C-T		not specified	Uncertain significance (Jan 04, 2024)
2-95048062-C-G		not specified	Uncertain significance (Aug 02, 2023)
2-95048091-G-C		not specified	Uncertain significance (Dec 21, 2023)
2-95049590-T-C		not specified	Uncertain significance (Apr 16, 2024)
2-95049623-G-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAL	protein_coding	protein_coding	ENST00000309988	4	28316

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.832	0.165	125744	0	2	125746	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.406	76	86.6	0.877	0.00000480	960
Missense in Polyphen		30	31.483	0.95289		375
Synonymous	-0.859	47	40.1	1.17	0.00000267	322
Loss of Function	2.25	0	5.88	0.00	2.50e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could be an important component in vesicular trafficking cycling between the Golgi complex and the apical plasma membrane. Could be involved in myelin biogenesis and/or myelin function.
• Pathway: role of mal in rho-mediated activation of srf (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.281
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.258

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mal
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: membrane raft polarization;protein localization to paranode region of axon;apoptotic process;central nervous system development;cell differentiation;myelination;apical protein localization;protein insertion into plasma membrane;positive regulation of extrinsic apoptotic signaling pathway via death domain receptors
• Cellular component: endoplasmic reticulum;integral component of membrane;apical plasma membrane;plasma membrane raft;membrane raft;hinge region between urothelial plaques of apical plasma membrane
• Molecular function: protein binding;lipid binding;peptidase activator activity involved in apoptotic process;structural constituent of myelin sheath