GALNT5

polypeptide N-acetylgalactosaminyltransferase 5, the group of Polypeptide N-acetylgalactosaminyltransferases

Basic information

Region (hg38): 2:157257704-157318491

Links

ENSG00000136542 ∙ NCBI:11227 ∙ OMIM:615129 ∙ HGNC:4127 ∙ Uniprot:Q7Z7M9 ∙ 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 GALNT5 gene.

• Inborn genetic diseases (41 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT5 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			37	5		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	5	0

Variants in GALNT5

This is a list of pathogenic ClinVar variants found in the GALNT5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-157258108-G-A		not specified	Uncertain significance (Dec 06, 2021)
2-157258176-G-A		not specified	Uncertain significance (May 15, 2023)
2-157258182-C-T		not specified	Uncertain significance (Sep 15, 2021)
2-157258243-G-A		not specified	Likely benign (Nov 30, 2022)
2-157258279-T-G		not specified	Uncertain significance (Feb 21, 2024)
2-157258326-G-C		not specified	Uncertain significance (Mar 16, 2022)
2-157258383-G-C		not specified	Uncertain significance (Dec 26, 2023)
2-157258405-C-A		not specified	Uncertain significance (Oct 03, 2022)
2-157258437-G-C		not specified	Uncertain significance (Oct 13, 2021)
2-157258455-C-T		not specified	Uncertain significance (May 03, 2023)
2-157258540-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-157258552-A-G		not specified	Uncertain significance (Sep 19, 2023)
2-157258560-C-T		not specified	Uncertain significance (Sep 23, 2023)
2-157258568-A-C		not specified	Uncertain significance (Jan 23, 2023)
2-157258576-C-T		not specified	Uncertain significance (Jun 01, 2023)
2-157258587-C-G		not specified	Uncertain significance (Sep 17, 2021)
2-157258632-A-G		not specified	Uncertain significance (May 18, 2023)
2-157258671-C-G		not specified	Likely benign (May 03, 2023)
2-157258674-C-T		not specified	Uncertain significance (Nov 12, 2021)
2-157258796-G-C		not specified	Uncertain significance (Oct 25, 2022)
2-157258851-A-C		not specified	Uncertain significance (Mar 06, 2023)
2-157258861-C-T		not specified	Uncertain significance (Feb 27, 2024)
2-157258920-A-C		not specified	Uncertain significance (Dec 28, 2023)
2-157258942-G-A		not specified	Likely benign (Aug 21, 2023)
2-157258977-G-A		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT5	protein_coding	protein_coding	ENST00000259056	10	56614

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.93e-14	0.633	125608	0	139	125747	0.000553

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.478	455	485	0.939	0.0000240	6172
Missense in Polyphen		157	161.69	0.971		2044
Synonymous	-0.380	182	176	1.04	0.00000880	1788
Loss of Function	1.64	26	36.8	0.707	0.00000196	460

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000791	0.000787
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.000693	0.000693
European (Non-Finnish)	0.000866	0.000853
Middle Eastern	0.0000548	0.0000544
South Asian	0.000196	0.000196
Other	0.000326	0.000326

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 EA2 peptide substrate, but has a weak activity toward Muc2 or Muc1b substrates (By similarity). {ECO:0000250}.
• 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: 0.0799

Intolerance Scores

• loftool: 0.861
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.9

Haploinsufficiency Scores

• pHI: 0.407
• hipred: N
• hipred_score: 0.144
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.707

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt5
• Phenotype: normal phenotype

Gene ontology

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