GALNTL5

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

Basic information

Region (hg38): 7:151956379-152019929

Previous symbols: [ "GALNT15" ]

Links

ENSG00000106648 ∙ NCBI:168391 ∙ OMIM:615133 ∙ HGNC:21725 ∙ Uniprot:Q7Z4T8 ∙ 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 GALNTL5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GALNTL5 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			43	3	3	49
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region					1	1
non coding					1	1
Total	0	0	44	3	5

Variants in GALNTL5

This is a list of pathogenic ClinVar variants found in the GALNTL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-151967257-C-T		not specified	Likely benign (Jul 12, 2022)
7-151967283-T-A		not specified	Uncertain significance (Aug 19, 2023)
7-151967341-T-A		not specified	Uncertain significance (Aug 02, 2023)
7-151967367-G-A		not specified	Uncertain significance (Aug 09, 2021)
7-151967392-G-GA		Male infertility	Likely pathogenic (Feb 09, 2021)
7-151967401-T-A		not specified	Uncertain significance (Oct 11, 2024)
7-151967412-A-G		not specified	Uncertain significance (Mar 07, 2023)
7-151967430-C-A		not specified	Uncertain significance (Jan 02, 2024)
7-151967473-A-G		not specified	Uncertain significance (Oct 07, 2024)
7-151967474-T-C		GALNTL5-related disorder	Likely benign (Jun 08, 2019)
7-151967478-G-A		not specified	Uncertain significance (Dec 13, 2023)
7-151970981-A-G		not specified	Uncertain significance (Oct 28, 2024)
7-151970992-A-C		not specified	Uncertain significance (Nov 22, 2021)
7-151971066-G-C			Benign (Dec 31, 2019)
7-151971074-T-C		GALNTL5-related disorder	Benign (Jul 16, 2018)
7-151982988-G-A		not specified	Uncertain significance (Aug 28, 2024)
7-151983009-C-A		not specified	Uncertain significance (Jun 26, 2024)
7-151983012-G-A		not specified	Uncertain significance (Apr 01, 2024)
7-151983015-T-C		not specified	Uncertain significance (Sep 08, 2024)
7-151983045-A-G			Benign (Apr 10, 2018)
7-151983117-A-G		not specified	Uncertain significance (Dec 07, 2021)
7-151983160-A-G			Benign (Aug 01, 2018)
7-151987161-G-A		not specified	Uncertain significance (Apr 25, 2022)
7-151987161-G-T		GALNTL5-related disorder	Benign (Apr 10, 2018)
7-151987162-A-G		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GALNTL5	protein_coding	protein_coding	ENST00000392800	8	63556

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.59e-16	0.00287	125525	1	222	125748	0.000887

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.792	270	236	1.15	0.0000119	2910
Missense in Polyphen		91	84.214	1.0806		1060
Synonymous	0.494	77	82.7	0.931	0.00000413	815
Loss of Function	-0.610	22	19.1	1.15	9.33e-7	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00257	0.00250
Ashkenazi Jewish	0.00915	0.00907
East Asian	0.00175	0.00169
Finnish	0.00	0.00
European (Non-Finnish)	0.000338	0.000325
Middle Eastern	0.00175	0.00169
South Asian	0.000382	0.000359
Other	0.000984	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable inactive glycosyltransferase required during spermatid development. May participate in protein loading into the acrosomes and accumulation of ubiquitin-proteasome systems around the head-tail coupling apparatus region.
• Disease: DISEASE: Note=Defects in GALNTL5 have been found in a patient with primary infertility due to asthenozoospermia. {ECO:0000269|PubMed:24398516}.
• Pathway: Mucin type O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.0700

Intolerance Scores

• loftool: 0.950
• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.92

Haploinsufficiency Scores

• pHI: 0.0338
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00408

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Galntl5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype

Gene ontology

• Biological process: protein glycosylation;spermatid development
• Cellular component: Golgi apparatus;integral component of membrane;late endosome membrane
• Molecular function: transferase activity, transferring glycosyl groups;metal ion binding