MAN1C1

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

Basic information

Region (hg38): 1:25616790-25786206

Links

ENSG00000117643 ∙ NCBI:57134 ∙ OMIM:616772 ∙ HGNC:19080 ∙ Uniprot:Q9NR34 ∙ 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 MAN1C1 gene.

• Inborn genetic diseases (17 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAN1C1 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			17		1	18
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	17	1	1

Variants in MAN1C1

This is a list of pathogenic ClinVar variants found in the MAN1C1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-25617837-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-25617865-T-C		not specified	Uncertain significance (Nov 06, 2023)
1-25617876-C-T		not specified	Uncertain significance (Feb 04, 2022)
1-25617963-C-G			Benign (Feb 09, 2018)
1-25617966-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-25618051-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-25618104-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-25618126-G-C		not specified	Uncertain significance (Jul 05, 2023)
1-25618152-G-A		not specified	Uncertain significance (Jan 10, 2022)
1-25618155-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-25618219-T-C		not specified	Uncertain significance (Jan 03, 2024)
1-25618272-A-G		not specified	Uncertain significance (Oct 02, 2023)
1-25618314-G-A		not specified	Uncertain significance (Oct 17, 2023)
1-25686470-C-T		not specified	Uncertain significance (Apr 20, 2023)
1-25686497-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-25749257-C-T		MAN1C1-related disorder	Benign (May 28, 2019)
1-25749278-G-A			Likely benign (Mar 01, 2023)
1-25753487-T-C		not specified	Uncertain significance (Nov 17, 2023)
1-25753491-G-A		not specified	Uncertain significance (Nov 21, 2022)
1-25753562-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-25753563-T-C		not specified	Uncertain significance (Dec 18, 2023)
1-25758615-C-T		not specified	Uncertain significance (Apr 27, 2023)
1-25763946-G-A		not specified	Uncertain significance (Sep 09, 2021)
1-25771726-G-A		not specified	Uncertain significance (Mar 06, 2023)
1-25771760-C-T		MAN1C1-related disorder	Likely benign (Jan 09, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAN1C1	protein_coding	protein_coding	ENST00000374332	12	168740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.209	0.791	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	278	368	0.756	0.0000209	4061
Missense in Polyphen		98	130.41	0.75148		1366
Synonymous	-0.757	173	161	1.08	0.0000101	1242
Loss of Function	4.06	8	33.3	0.240	0.00000189	344

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000305
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000229	0.000229
Other	0.000187	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the maturation of Asn-linked oligosaccharides. Trim alpha-1,2-linked mannose residues from Man(9)GlcNAc(2) to produce first Man(8)GlcNAc(2) then Man(6)GlcNAc and a small amount of Man(5)GlcNAc.
• 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: 0.109

Intolerance Scores

• loftool: 0.342
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.51

Haploinsufficiency Scores

• pHI: 0.152
• hipred: Y
• hipred_score: 0.597
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.236

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Man1c1

Gene ontology

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