GALNT10

polypeptide N-acetylgalactosaminyltransferase 10, the group of Polypeptide N-acetylgalactosaminyltransferases|MicroRNA protein coding host genes

Basic information

Region (hg38): 5:154190729-154420984

Links

ENSG00000164574 ∙ NCBI:55568 ∙ OMIM:608043 ∙ HGNC:19873 ∙ Uniprot:Q86SR1 ∙ 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 GALNT10 gene.

• Inborn genetic diseases (24 variants)
• not specified (2 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT10 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					1	1
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	24	1	3

Variants in GALNT10

This is a list of pathogenic ClinVar variants found in the GALNT10 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-154191000-C-G		not specified	Uncertain significance (May 27, 2022)
5-154294819-T-A		not specified	Uncertain significance (Nov 22, 2023)
5-154294912-C-T		not specified	Uncertain significance (Oct 12, 2022)
5-154297802-G-C		not specified	Benign (-)
5-154297803-A-T		not specified	Benign (-)
5-154329585-C-T		not specified	Uncertain significance (Apr 07, 2023)
5-154329658-G-T		not specified	Uncertain significance (Jul 20, 2021)
5-154329663-G-A		not specified	Uncertain significance (Sep 01, 2021)
5-154329679-A-G		not specified	Uncertain significance (Aug 13, 2021)
5-154329693-G-C		not specified	Uncertain significance (May 27, 2022)
5-154329699-G-C		not specified	Uncertain significance (Jul 13, 2022)
5-154329721-A-C		not specified	Uncertain significance (Feb 22, 2023)
5-154376306-A-G		not specified	Uncertain significance (Apr 06, 2022)
5-154376312-C-T		not specified	Uncertain significance (Jun 09, 2022)
5-154376348-C-T		not specified	Uncertain significance (Mar 25, 2022)
5-154376390-G-T		not specified	Uncertain significance (Aug 12, 2021)
5-154380499-T-C		not specified	Uncertain significance (Dec 06, 2021)
5-154380516-C-T		not specified	Uncertain significance (Sep 13, 2023)
5-154380547-G-A		not specified	Uncertain significance (Aug 17, 2022)
5-154380579-C-T		not specified	Uncertain significance (Feb 06, 2024)
5-154380592-C-T		not specified	Uncertain significance (Feb 21, 2024)
5-154404123-G-A		not specified	Uncertain significance (Feb 13, 2024)
5-154409732-C-T		GALNT10-related disorder	Likely benign (Oct 03, 2022)
5-154409733-G-A		not specified	Uncertain significance (Nov 17, 2022)
5-154412893-G-A			Likely benign (Mar 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT10	protein_coding	protein_coding	ENST00000297107	12	230255

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000199	1.00	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	292	375	0.778	0.0000238	3944
Missense in Polyphen		130	178.44	0.72853		1880
Synonymous	0.110	144	146	0.988	0.00000922	1170
Loss of Function	3.22	14	34.3	0.408	0.00000201	340

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.000164	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 Muc5Ac and EA2 peptide substrates.
• 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: 0.112

Intolerance Scores

• loftool: 0.651
• rvis_EVS: -1.2
• rvis_percentile_EVS: 5.79

Haploinsufficiency Scores

• pHI: 0.659
• hipred: Y
• hipred_score: 0.706
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.560

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt10
• Phenotype: normal phenotype

Gene ontology

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