GALNT17

polypeptide N-acetylgalactosaminyltransferase 17, the group of Polypeptide N-acetylgalactosaminyltransferases|MicroRNA protein coding host genes

Basic information

Region (hg38): 7:71132143-71713600

Previous symbols: [ "WBSCR17" ]

Links

ENSG00000185274 ∙ NCBI:64409 ∙ OMIM:615137 ∙ HGNC:16347 ∙ Uniprot:Q6IS24 ∙ 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 GALNT17 gene.

• Inborn genetic diseases (6 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT17 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	6	0	2

Variants in GALNT17

This is a list of pathogenic ClinVar variants found in the GALNT17 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-71132840-T-G		not specified	Uncertain significance (Apr 07, 2023)
7-71132893-A-G		not specified	Uncertain significance (Jan 03, 2024)
7-71132984-A-G		not specified	Uncertain significance (Sep 15, 2021)
7-71335562-C-T		not specified	Uncertain significance (Dec 15, 2023)
7-71335580-G-A		not specified	Uncertain significance (Oct 05, 2023)
7-71335592-G-A		not specified	Uncertain significance (Nov 15, 2021)
7-71335610-C-T		not specified	Uncertain significance (Jun 01, 2023)
7-71335709-C-G		not specified	Uncertain significance (Aug 17, 2022)
7-71388309-C-T		not specified	Uncertain significance (Oct 02, 2023)
7-71388338-G-A		not specified	Uncertain significance (Jan 07, 2022)
7-71388395-G-A		not specified	Uncertain significance (Sep 12, 2023)
7-71388410-G-A			Benign (Nov 06, 2018)
7-71415933-C-T		not specified	Uncertain significance (Jan 24, 2024)
7-71415936-G-A		not specified	Uncertain significance (Jul 15, 2021)
7-71415948-G-A		not specified	Uncertain significance (May 30, 2022)
7-71416012-C-G		not specified	Uncertain significance (Jul 14, 2022)
7-71420928-G-A		not specified	Uncertain significance (Sep 26, 2023)
7-71420963-T-G		not specified	Uncertain significance (Oct 26, 2022)
7-71420984-G-A		not specified	Uncertain significance (Feb 26, 2024)
7-71421062-C-G		not specified	Uncertain significance (Jun 22, 2023)
7-71665471-C-T		not specified	Uncertain significance (Sep 17, 2021)
7-71665590-G-A			Benign (Nov 06, 2018)
7-71670095-G-A		not specified	Likely benign (May 11, 2022)
7-71710800-G-A		not specified	Uncertain significance (Feb 16, 2023)
7-71710860-C-T		not specified	Uncertain significance (Dec 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT17	protein_coding	protein_coding	ENST00000333538	11	581431

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.117	0.883	125736	0	9	125745	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	243	376	0.646	0.0000233	3886
Missense in Polyphen		68	139.14	0.48873		1391
Synonymous	1.05	139	156	0.893	0.0000101	1177
Loss of Function	3.57	7	27.0	0.259	0.00000115	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000636	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000271	0.0000264
Middle Eastern	0.0000550	0.0000544
South Asian	0.0000984	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May catalyze 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. {ECO:0000250|UniProtKB:Q9HCQ5}.
• Disease: DISEASE: Note=WBSCR17 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.
• 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: 0.113

Intolerance Scores

• rvis_EVS: -1.22
• rvis_percentile_EVS: 5.57

Haploinsufficiency Scores

• pHI: 0.611
• hipred: Y
• hipred_score: 0.725
• ghis: 0.640

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Galnt17
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

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