AMY1C

amylase alpha 1C, the group of Amylases alpha

Basic information

Region (hg38): 1:103745323-103758726

Previous symbols: [ "AMY1" ]

Links

ENSG00000187733 ∙ NCBI:278 ∙ OMIM:104702 ∙ HGNC:476 ∙ Uniprot:P0DTE8 ∙ 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 AMY1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMY1C 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in AMY1C

This is a list of pathogenic ClinVar variants found in the AMY1C region.

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

Position	Type	Phenotype	Significance	ClinVar
1-103754525-T-C		not specified	Uncertain significance (Jun 14, 2022)
1-103754768-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-103754785-C-T		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMY1C	protein_coding	protein_coding	ENST00000370079	10	8285

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00340	0.631	122078	1	1879	123958	0.00761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.503	46	37.4	1.23	0.00000200	3357
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00828	0.00809
Ashkenazi Jewish	0.00596	0.00520
East Asian	0.00110	0.00109
Finnish	0.00965	0.00868
European (Non-Finnish)	0.0132	0.0114
Middle Eastern	0.00110	0.00109
South Asian	0.00379	0.00349
Other	0.00896	0.00765

dbNSFP

Source: dbNSFP

• Pathway: 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;Mucopolysaccharidosis VI. Sly syndrome;Sucrase-isomaltase deficiency;Glycogenosis, Type IV. Amylopectinosis, Anderson disease;Glycogenosis, Type VI. Hers disease;Starch and Sucrose Metabolism;Digestion of dietary carbohydrate;Endohydrolysis of 1,4-alpha-D-glucosidic linkages in polysaccharides by alpha-amylase;Digestion;Digestion and absorption (Consensus)

Recessive Scores

• pRec: 0.376

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.906

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amy2a5