MAL2

mal, T cell differentiation protein 2, the group of MARVEL domain containing

Basic information

Region (hg38): 8:119165033-119245673

Links

ENSG00000147676 ∙ NCBI:114569 ∙ OMIM:609684 ∙ HGNC:13634 ∙ Uniprot:Q969L2 ∙ 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 MAL2 gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAL2 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in MAL2

This is a list of pathogenic ClinVar variants found in the MAL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-119208483-G-T		not specified	Uncertain significance (Nov 15, 2023)
8-119208515-G-A		not specified	Uncertain significance (Jan 06, 2023)
8-119240301-A-G		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAL2	protein_coding	protein_coding	ENST00000276681	5	80641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.137	0.787	124645	0	6	124651	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.496	67	79.4	0.843	0.00000411	1085
Missense in Polyphen		28	42.269	0.66243		525
Synonymous	0.0890	33	33.7	0.980	0.00000205	349
Loss of Function	1.43	2	5.69	0.351	2.41e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000354
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Member of the machinery of polarized transport. Required for the indirect transcytotic route at the step of the egress of the transcytosing cargo from perinuclear endosomes in order for it to travel to the apical surface via a raft-dependent pathway. {ECO:0000269|PubMed:12370246}.

Recessive Scores

• pRec: 0.133

Haploinsufficiency Scores

• pHI: 0.669
• hipred: N
• hipred_score: 0.310

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.852

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mal2

Gene ontology

• Biological process: myelination;transcytosis
• Cellular component: endomembrane system;integral component of membrane;apical plasma membrane;membrane raft;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding;structural constituent of myelin sheath