MAN1A1

mannosidase alpha class 1A member 1, the group of Mannosidases alpha class 1

Basic information

Region (hg38): 6:119177205-119349761

Links

ENSG00000111885 ∙ NCBI:4121 ∙ OMIM:604344 ∙ HGNC:6821 ∙ Uniprot:P33908 ∙ 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 MAN1A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAN1A1 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					1	1
missense			28		1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	28	0	2

Variants in MAN1A1

This is a list of pathogenic ClinVar variants found in the MAN1A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-119179830-T-C			Benign (Dec 31, 2019)
6-119179832-A-T		not specified	Uncertain significance (Apr 24, 2024)
6-119179839-C-G		not specified	Uncertain significance (Oct 02, 2023)
6-119179904-A-G		not specified	Uncertain significance (Jun 17, 2022)
6-119179920-C-T		not specified	Uncertain significance (Jan 08, 2024)
6-119180367-G-A		not specified	Uncertain significance (Sep 23, 2023)
6-119188433-T-A		not specified	Uncertain significance (Feb 05, 2024)
6-119188496-A-T		not specified	Uncertain significance (Oct 18, 2021)
6-119189674-A-G			Benign (Dec 31, 2019)
6-119189694-G-C		not specified	Uncertain significance (Jan 16, 2024)
6-119189778-C-T		not specified	Uncertain significance (Mar 25, 2024)
6-119189810-A-G		not specified	Uncertain significance (Oct 12, 2021)
6-119189840-G-C		not specified	Uncertain significance (Nov 18, 2022)
6-119189847-C-T		not specified	Uncertain significance (Aug 17, 2021)
6-119189880-T-C		not specified	Uncertain significance (Jan 17, 2023)
6-119193769-T-C			Benign (Dec 31, 2019)
6-119193811-A-G		not specified	Uncertain significance (Jan 20, 2023)
6-119201268-C-T		not specified	Uncertain significance (May 27, 2022)
6-119248323-A-G		not specified	Uncertain significance (May 31, 2022)
6-119290706-C-T		not specified	Uncertain significance (Feb 10, 2022)
6-119301999-C-G		not specified	Uncertain significance (Mar 21, 2024)
6-119302003-A-C		not specified	Uncertain significance (Jan 23, 2024)
6-119302013-A-C		not specified	Uncertain significance (Dec 21, 2022)
6-119348518-T-C		not specified	Uncertain significance (Mar 11, 2022)
6-119348750-C-T		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAN1A1	protein_coding	protein_coding	ENST00000368468	12	172553

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.111	0.889	125731	0	15	125746	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	270	350	0.772	0.0000171	4244
Missense in Polyphen		81	154.55	0.52411		1882
Synonymous	0.780	126	138	0.915	0.00000712	1266
Loss of Function	3.86	8	31.3	0.256	0.00000161	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000553	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000445	0.0000440
Middle Eastern	0.0000553	0.0000544
South Asian	0.0000689	0.0000653
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the maturation of Asn-linked oligosaccharides. Progressively trim alpha-1,2-linked mannose residues from Man(9)GlcNAc(2) to produce Man(5)GlcNAc(2).
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);N-Glycan biosynthesis - Homo sapiens (human);Vesicle-mediated transport;er associated degradation (erad) pathway;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;N-glycan trimming and elongation in the cis-Golgi;Progressive trimming of alpha-1,2-linked mannose residues from Man9/8/7GlcNAc2 to produce Man5GlcNAc2;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Intra-Golgi traffic;N-Glycan biosynthesis;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.515
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.0395
• hipred: Y
• hipred_score: 0.625
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Man1a

Gene ontology

• Biological process: protein glycosylation;N-glycan processing;Golgi apparatus mannose trimming
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cytosol;membrane;integral component of membrane;extracellular exosome
• Molecular function: mannosyl-oligosaccharide 1,2-alpha-mannosidase activity;calcium ion binding;mannosidase activity