GALNT14

polypeptide N-acetylgalactosaminyltransferase 14, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 2:30910466-31155202

Links

ENSG00000158089 ∙ NCBI:79623 ∙ OMIM:608225 ∙ HGNC:22946 ∙ Uniprot:Q96FL9 ∙ 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 GALNT14 gene.

• Inborn genetic diseases (33 variants)
• not provided (4 variants)
• Non-immune hydrops fetalis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT14 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					2	2
missense			32	1	1	34
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	1	32	1	4

Highest pathogenic variant AF is 0.0000591

Variants in GALNT14

This is a list of pathogenic ClinVar variants found in the GALNT14 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-30910913-C-A		not specified	Uncertain significance (Feb 13, 2024)
2-30910944-T-C		not specified	Uncertain significance (Aug 17, 2022)
2-30910957-C-A		not specified	Uncertain significance (May 06, 2022)
2-30910960-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-30910961-G-C		GALNT14-related disorder	Uncertain significance (Nov 08, 2023)
2-30910969-T-C		not specified	Uncertain significance (Jan 04, 2024)
2-30910990-C-T		not specified	Uncertain significance (Oct 12, 2022)
2-30911005-C-G		not specified	Uncertain significance (Nov 08, 2022)
2-30912229-G-A			Benign (Mar 27, 2018)
2-30912258-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-30912267-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-30924132-T-C		not specified	Uncertain significance (Oct 03, 2022)
2-30924219-C-T		not specified	Uncertain significance (Apr 05, 2023)
2-30924223-G-C		not specified	Uncertain significance (Mar 29, 2023)
2-30924226-G-A		Non-immune hydrops fetalis	Pathogenic/Likely pathogenic (Mar 25, 2024)
2-30924237-T-C		not specified	Uncertain significance (Sep 20, 2023)
2-30924789-G-A		not specified	Uncertain significance (Jun 21, 2023)
2-30929399-C-T		not specified	Uncertain significance (Feb 10, 2022)
2-30929432-C-A		not specified	Uncertain significance (Feb 16, 2023)
2-30929483-T-C		not specified	Uncertain significance (Nov 08, 2022)
2-30932077-G-A		not specified	Uncertain significance (Dec 06, 2022)
2-30932119-C-T		not specified	Uncertain significance (Apr 20, 2023)
2-30932137-C-T		not specified	Uncertain significance (Jan 02, 2024)
2-30932150-C-T		GALNT14-related disorder	Likely benign (Apr 10, 2023)
2-30942270-C-T		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT14	protein_coding	protein_coding	ENST00000324589	16	244736

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.06e-17	0.104	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.435	312	334	0.933	0.0000198	3652
Missense in Polyphen		130	148.1	0.87779		1581
Synonymous	0.218	130	133	0.976	0.00000813	1055
Loss of Function	1.09	29	36.0	0.805	0.00000195	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000788	0.000788
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000762	0.000761
Finnish	0.00	0.00
European (Non-Finnish)	0.000433	0.000431
Middle Eastern	0.000762	0.000761
South Asian	0.0000981	0.0000980
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. Displays activity toward mucin-derived peptide substrates such as Muc2, Muc5AC, Muc7, and Muc13 (-58). May be involved in O-glycosylation in kidney.
• 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: 0.0913

Intolerance Scores

• loftool: 0.864
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.66

Haploinsufficiency Scores

• pHI: 0.0665
• hipred: N
• hipred_score: 0.306
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt14
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

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