GALNT11

polypeptide N-acetylgalactosaminyltransferase 11, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 7:152025674-152122340

Links

ENSG00000178234 ∙ NCBI:63917 ∙ OMIM:615130 ∙ HGNC:19875 ∙ Uniprot:Q8NCW6 ∙ 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 GALNT11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT11 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			24	4	2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	4	2

Variants in GALNT11

This is a list of pathogenic ClinVar variants found in the GALNT11 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-152094246-C-T		not specified	Uncertain significance (May 27, 2022)
7-152094280-C-T		GALNT11-related disorder	Likely benign (May 03, 2018)
7-152094376-C-T		not specified	Uncertain significance (Aug 28, 2024)
7-152094399-C-T		not specified	Uncertain significance (Aug 01, 2024)
7-152094409-G-A		not specified	Uncertain significance (Aug 12, 2021)
7-152094423-G-C		not specified	Likely benign (Aug 03, 2022)
7-152094424-T-C		not specified	Uncertain significance (Sep 04, 2024)
7-152094433-C-T		not specified	Uncertain significance (Oct 22, 2024)
7-152094468-G-A		not specified	Uncertain significance (Sep 26, 2024)
7-152100800-A-G		not specified	Uncertain significance (Feb 28, 2023)
7-152100810-A-C		not specified	Uncertain significance (Oct 17, 2024)
7-152100888-A-G		not specified	Uncertain significance (Apr 26, 2023)
7-152103124-G-C		not specified	Uncertain significance (Mar 15, 2023)
7-152103143-C-T			Benign (Sep 11, 2018)
7-152103150-C-G		not specified	Uncertain significance (Aug 01, 2024)
7-152103203-G-A		not specified	Uncertain significance (Sep 06, 2022)
7-152103207-A-G		not specified	Uncertain significance (Sep 20, 2023)
7-152103221-C-G		not specified	Uncertain significance (Mar 29, 2024)
7-152105269-A-G		not specified	Uncertain significance (May 20, 2024)
7-152105271-T-C		not specified	Uncertain significance (Nov 13, 2024)
7-152105274-G-A		not specified	Likely benign (Feb 06, 2023)
7-152105309-A-G		not specified	Uncertain significance (May 04, 2023)
7-152105325-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-152105356-C-T		not specified	Uncertain significance (Jul 25, 2024)
7-152105359-C-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT11	protein_coding	protein_coding	ENST00000434507	11	96667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000167	1.00	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.896	322	371	0.869	0.0000221	3976
Missense in Polyphen		112	146.24	0.76585		1600
Synonymous	0.0630	140	141	0.993	0.00000870	1167
Loss of Function	3.16	14	33.9	0.413	0.00000210	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000364	0.000364
Ashkenazi Jewish	0.00	0.00
East Asian	0.000275	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.000275	0.000272
South Asian	0.0000335	0.0000327
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Polypeptide N-acetylgalactosaminyltransferase that catalyzes the initiation of protein O-linked glycosylation and is involved in left/right asymmetry by mediating O-glycosylation of NOTCH1. O-glycosylation of NOTCH1 promotes activation of NOTCH1, modulating the balance between motile and immotile (sensory) cilia at the left-right organiser (LRO). Polypeptide N- acetylgalactosaminyltransferases catalyze the transfer of an N- acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Displays the same enzyme activity toward MUC1, MUC4, and EA2 than GALNT1. Not involved in glycosylation of erythropoietin (EPO). {ECO:0000269|PubMed:11925450, ECO:0000269|PubMed:24226769}.
• Disease: DISEASE: Note=Defects in GALNT11 may be a cause of heterotaxy, a congenital heart disease resulting from abnormalities in left- right (LR) body patterning. {ECO:0000269|PubMed:21282601}.
• 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: 0.101

Intolerance Scores

• loftool: 0.412
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.63

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.416
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt11

Gene ontology

• Biological process: Notch receptor processing;determination of left/right symmetry;regulation of Notch signaling pathway;O-glycan processing;protein O-linked glycosylation via threonine;cilium assembly;Notch signaling involved in heart development
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: polypeptide N-acetylgalactosaminyltransferase activity;Notch binding;carbohydrate binding;metal ion binding