GALNT7

polypeptide N-acetylgalactosaminyltransferase 7, the group of Polypeptide N-acetylgalactosaminyltransferases|MicroRNA protein coding host genes

Basic information

Region (hg38): 4:173168811-173323967

Links

ENSG00000109586 ∙ NCBI:51809 ∙ OMIM:605005 ∙ HGNC:4129 ∙ Uniprot:Q86SF2 ∙ 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 GALNT7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNT7 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	2

Variants in GALNT7

This is a list of pathogenic ClinVar variants found in the GALNT7 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-173168924-C-A		not specified	Uncertain significance (Nov 27, 2024)
4-173168942-G-A		not specified	Uncertain significance (Jun 28, 2024)
4-173248002-C-T		not specified	Uncertain significance (Jan 22, 2025)
4-173248014-G-A		not specified	Uncertain significance (Jan 08, 2025)
4-173248025-G-A		not specified	Uncertain significance (Feb 03, 2025)
4-173248086-T-C		not specified	Uncertain significance (Sep 14, 2023)
4-173248095-A-G		not specified	Uncertain significance (Aug 12, 2021)
4-173248130-A-T		not specified	Uncertain significance (May 24, 2023)
4-173248145-C-T		not specified	Uncertain significance (Sep 15, 2021)
4-173248242-G-A		not specified	Uncertain significance (Jan 17, 2025)
4-173248250-G-A		not specified	Uncertain significance (Apr 24, 2023)
4-173248412-C-T		not specified	Uncertain significance (Sep 11, 2024)
4-173248418-G-A		not specified	Uncertain significance (Jun 22, 2022)
4-173248433-C-G		not specified	Uncertain significance (Sep 21, 2023)
4-173248438-A-C		not specified	Uncertain significance (Feb 03, 2022)
4-173292151-G-A		not specified	Uncertain significance (Jan 07, 2022)
4-173292214-A-G		not specified	Uncertain significance (Jan 15, 2025)
4-173292223-C-G		not specified	Uncertain significance (Aug 16, 2021)
4-173295403-A-T		not specified	Uncertain significance (Dec 03, 2021)
4-173295437-A-C		not specified	Uncertain significance (Dec 21, 2022)
4-173295818-C-T		not specified	Uncertain significance (May 30, 2024)
4-173295822-T-C		not specified	Uncertain significance (Nov 25, 2024)
4-173298138-T-C		not specified	Uncertain significance (Oct 17, 2023)
4-173298240-G-A		not specified	Uncertain significance (Mar 25, 2024)
4-173298287-G-C		not specified	Uncertain significance (Jan 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNT7	protein_coding	protein_coding	ENST00000265000	12	155215

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000259	1.00	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	266	362	0.735	0.0000182	4326
Missense in Polyphen		83	133.61	0.62121		1544
Synonymous	1.80	101	127	0.796	0.00000655	1208
Loss of Function	3.28	16	37.7	0.424	0.00000207	430

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000326
Ashkenazi Jewish	0.00	0.00
East Asian	0.000117	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000207	0.000202
Middle Eastern	0.000117	0.000109
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycopeptide transferase involved in O-linked oligosaccharide biosynthesis, which catalyzes the transfer of an N-acetyl-D-galactosamine residue to an already glycosylated peptide. In contrast to other proteins of the family, it does not act as a peptide transferase that transfers GalNAc onto serine or threonine residue on the protein receptor, but instead requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. Some peptide transferase activity is however not excluded, considering that its appropriate peptide substrate may remain unidentified.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;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: 0.110

Intolerance Scores

• loftool: 0.856
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.85

Haploinsufficiency Scores

• pHI: 0.242
• hipred: Y
• hipred_score: 0.639
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.236

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galnt7

Gene ontology

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