GALNT12

polypeptide N-acetylgalactosaminyltransferase 12, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 9:98807669-98850081

Links

ENSG00000119514 ∙ NCBI:79695 ∙ OMIM:610290 ∙ HGNC:19877 ∙ Uniprot:Q8IXK2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• colorectal cancer, susceptibility to, 1 (Limited), mode of inheritance: AD
• colorectal cancer, susceptibility to, 1 (Limited), mode of inheritance: AD
• colorectal cancer, susceptibility to, 1 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Colorectal cancer, susceptibility to, 1	AD	Oncologic	Surveillance for colorectal neoplasms may allow early diagnosis and treatment of tumors, which may reduce morbidity and mortality	Oncologic	19617566; 22461326

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GALNT12 gene.

• Hereditary cancer-predisposing syndrome (1056 variants)
• not provided (577 variants)
• Colorectal cancer, susceptibility to, 1 (117 variants)
• not specified (16 variants)
• Inborn genetic diseases (4 variants)
• GALNT12-related condition (3 variants)
• Adenomatous polyposis coli, attenuated (1 variants)
• Familial colorectal cancer (1 variants)
• Colorectal cancer (1 variants)
• Breast neoplasm (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT12 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			5	297	2	304
missense			713	21	2	736
nonsense			28			28
start loss			6			6
frameshift			32			32
inframe indel			17			17
splice donor/acceptor (+/-2bp)			13			13
splice region			16	13	1	30
non coding			5	30	25	60
Total	0	0	819	348	29

Variants in GALNT12

This is a list of pathogenic ClinVar variants found in the GALNT12 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-98807689-T-C		GALNT12-related disorder	Likely benign (Jan 10, 2022)
9-98807690-G-A		GALNT12-related disorder	Likely benign (Jan 10, 2022)
9-98807692-CGGGCGCATGTGG-C			Uncertain significance (Dec 11, 2019)
9-98807692-C-CGGGCGCATGTGG		not specified	Uncertain significance (Oct 14, 2021)
9-98807694-G-A		not specified	Uncertain significance (Jan 07, 2022)
9-98807695-GC-A		not specified	Uncertain significance (Mar 12, 2019)
9-98807696-C-A		not specified	Uncertain significance (Nov 25, 2019)
9-98807697-G-A		not specified	Uncertain significance (Apr 21, 2022)
9-98807698-C-T		not specified	Uncertain significance (Sep 11, 2023)
9-98807699-A-C		not specified	Uncertain significance (Nov 22, 2023)
9-98807699-A-G		not specified	Uncertain significance (Dec 04, 2023)
9-98807699-A-T		not specified	Uncertain significance (Aug 04, 2021)
9-98807700-T-C		not specified	Conflicting classifications of pathogenicity (Aug 03, 2022)
9-98807701-G-A		Colorectal cancer, susceptibility to, 1 • not specified	Uncertain significance (Dec 21, 2023)
9-98807701-G-T		not specified	Uncertain significance (Jun 06, 2023)
9-98807702-T-TG		Colorectal cancer, susceptibility to, 1	Uncertain significance (Sep 11, 2023)
9-98807703-G-A		not specified	Uncertain significance (Aug 28, 2023)
9-98807703-G-C		not specified	Uncertain significance (Dec 22, 2023)
9-98807703-G-T		Hereditary cancer-predisposing syndrome	Uncertain significance (Nov 06, 2023)
9-98807702-T-TTG		not specified	Uncertain significance (Dec 03, 2019)
9-98807704-G-T		Colorectal cancer, susceptibility to, 1	Uncertain significance (Jun 26, 2023)
9-98807705-G-C		not specified	Uncertain significance (May 17, 2023)
9-98807706-G-A		not specified	Uncertain significance (Aug 01, 2023)
9-98807707-G-T		not specified	Likely benign (Oct 29, 2020)
9-98807708-C-T		not specified	Uncertain significance (May 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT12	protein_coding	protein_coding	ENST00000375011	10	42383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.39e-7	0.931	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.131	272	278	0.978	0.0000172	3735
Missense in Polyphen		151	150.64	1.0024		1775
Synonymous	0.143	112	114	0.983	0.00000757	1156
Loss of Function	1.77	13	22.0	0.592	9.66e-7	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000489	0.000489
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000272	0.000272
South Asian	0.000134	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D- galactosamine residue to a serine or threonine residue on the protein receptor. Has activity toward non-glycosylated peptides such as Muc5AC, Muc1a and EA2, and no detectable activity with Muc2 and Muc7. Displays enzymatic activity toward the Gal-NAc- Muc5AC glycopeptide, but no detectable activity to mono-GalNAc- glycosylated Muc1a, Muc2, Muc7 and EA2. May play an important role in the initial step of mucin-type oligosaccharide biosynthesis in digestive organs.
• Disease: DISEASE: Colorectal cancer 1 (CRCS1) [MIM:608812]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. {ECO:0000269|PubMed:19617566, ECO:0000269|PubMed:22461326, ECO:0000269|PubMed:24115450}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. The role of GALNT12 in colon cancer susceptibility is however subject to discussion: studies on 103 probants with colorectal cancer 1 (CRCS1) suggest that it does not act as a major contributor of CRCS1 (PubMed:24115450). {ECO:0000269|PubMed:24115450}.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;O-Glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.672
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.08

Haploinsufficiency Scores

• pHI: 0.530
• hipred: Y
• hipred_score: 0.651
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.780

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt12

Gene ontology

• Biological process: O-glycan processing
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: polypeptide N-acetylgalactosaminyltransferase activity;carbohydrate binding;metal ion binding