MAN1C1

protein-coding

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

Gene summary

Predicted to enable mannosyl-oligosaccharide 1,2-alpha-mannosidase activity. Predicted to be involved in ERAD pathway. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020379.4

Inheritance

—

ClinVar variants

U:92B:9

Top phenotype

MAN1C1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr1:25,616,791-25,784,450

External References & Databases

Ensembl (ENSG00000117643)

Transcript & Mutation Effects

hg38 • Region Span ~167.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAN1C1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 85

MAN1C1-related disorderTotal: 9

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020379.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	7 clinvar	1 clinvar	12
missense			87 clinvar		1 clinvar	88
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	92	7	2	101

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020379.4	RefSeq	NP_065112.1	12	MANE Select
ENST00000374332.9	Ensembl	ENSP00000363452.4	12	MANE Select
NM_001289010.2	RefSeq	NP_001275939.1	12	Standard
NM_001385182.1	RefSeq	NP_001372111.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein processing in endoplasmic reticulum - Homo sapiens (human)
N-Glycan biosynthesis - Homo sapiens (human)
Vesicle-mediated transport
er associated degradation (erad) pathway
Membrane Trafficking

Biological Process

protein N-linked glycosylation
N-glycan processing
Golgi apparatus mannose trimming

Molecular Function

mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
calcium ion binding

Cellular Component

Golgi membrane
endoplasmic reticulum
integral component of Golgi membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374332
Coding exons: 12
Length: 168740
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.66	278	368	0.756	0.0000209	4061
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00023	0.00023	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.342
RVIS EVS: -0.47
RVIS percentile EVS: 23.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.236

Gene Damage Prediction

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