GALNTL5

protein-coding

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

Gene summary

Predicted to enable metal ion binding activity and transferase activity. Involved in spermatid development. Predicted to be located in late endosome membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

GALNT15

MANE transcript

NM_145292.4

Inheritance

—

ClinVar variants

P:1U:76B:11

Top phenotype

GALNTL5-related disorder

gnomAD constraint

pLI —, LoF o/e 1.15

Max pathogenic AF

—

Genomic locus

chr7:151,956,379-152,019,929

External References & Databases

Ensembl (ENSG00000106648)

Transcript & Mutation Effects

hg38 • Region Span ~63.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GALNTL5 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 78

not providedTotal: 8

GALNTL5-related disorderTotal: 7

Male infertilityTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145292.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			75 clinvar	6 clinvar	3 clinvar	84
nonsense						0
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)					1 clinvar	1
Total	0	1	76	7	4	88

Highest pathogenic variant AF is 0.000008675091

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145292.4	RefSeq	NP_660335.2	8	MANE Select
ENST00000392800.7	Ensembl	ENSP00000376548.2	8	MANE Select
ENST00000414073.6	Ensembl	ENSP00000414260.2	3	Standard
ENST00000416062.5	Ensembl	ENSP00000411071.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mucin type O-glycan biosynthesis - Homo sapiens (human)
Post-translational protein modification
Metabolism of proteins
O-linked glycosylation of mucins
O-linked glycosylation

Biological Process

protein glycosylation
spermatid development

Molecular Function

transferase activity, transferring glycosyl groups
metal ion binding

Cellular Component

Golgi apparatus
integral component of membrane
late endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392800
Coding exons: 8
Length: 63556
Individuals with no LoFs: 125525
Homozygous LoFs: 1
Heterozygous LoFs: 222
Defined: 125748
p: 0.000887

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.792	270	236	1.15	0.0000119	2910
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0022	0.0022	notable
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0.0092	0.0091	notable
East Asian	0.0018	0.0017	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00034	0.00033	rare
South Asian	0.00038	0.00036	rare
Other	0.00098	0.00098	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0700

Intolerance Scores

LoFtool: 0.950
RVIS EVS: 1.42
RVIS percentile EVS: 94.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00408

Gene Damage Prediction

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