AMY1C

protein-coding

amylase alpha 1C, the group of Amylases alpha

Gene summary

Amylases are secreted proteins that hydrolyze 1,4-alpha-glucoside bonds in oligosaccharides and polysaccharides, and thus catalyze the first step in digestion of dietary starch and glycogen. The human genome has a cluster of several amylase genes that are expressed at high levels in either salivary gland or pancreas. This gene encodes an amylase isoenzyme produced by the salivary gland. [provided by RefSeq, Jul 2008]

Previous symbols:

AMY1

MANE transcript

NM_001008219.3

Inheritance

—

ClinVar variants

U:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr1:103,745,323-103,758,726

External References & Databases

Ensembl (ENSG00000187733)

Transcript & Mutation Effects

hg38 • Region Span ~13.4 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 AMY1C variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001008219.3. 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						0
missense			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	0	0	9

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001008219.3	RefSeq	NP_001008220.1	10	MANE Select
ENST00000622339.5	Ensembl	ENSP00000481450.2	10	MANE Select
NM_001346780.1	RefSeq	NP_001333709.1	10	Standard
ENST00000370079.3	Ensembl	ENSP00000359096.3	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Starch and sucrose metabolism - Homo sapiens (human)
Carbohydrate digestion and absorption - Homo sapiens (human)
Salivary secretion - Homo sapiens (human)
Glycogen synthetase deficiency
Glycogenosis, Type III. Cori disease, Debrancher glycogenosis

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370079
Coding exons: 10
Length: 8285
Individuals with no LoFs: 122078
Homozygous LoFs: 1
Heterozygous LoFs: 1879
Defined: 123958
p: 0.00761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.503	46	37.4	1.23	0.00000200	3357
Missense (PolyPhen)		20	19.237	1.0397		1532
Synonymous	0.433	10	11.9	0.840	6.74e-7	916
Loss of Function	0.495	4	5.22	0.766	3.21e-7	281

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0021	notable
Latino/Admixed American	0.0060	0.0050	notable
Ashkenazi Jewish	0.0060	0.0052	notable
East Asian	0.0011	0.0011	notable
Finnish	0.0096	0.0087	notable
European (Non-Finnish)	0.013	0.011	notable
South Asian	0.0038	0.0035	notable
Other	0.0090	0.0077	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.376

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.906

Gene Damage Prediction

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