NLGN4Y

neuroligin 4 Y-linked, the group of Neuroligins

Basic information

Region (hg38): Y:14522573-14845654

Links

ENSG00000165246

∙ NCBI:22829 ∙ OMIM:400028 ∙ HGNC:15529 ∙ Uniprot:Q8NFZ3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

male infertility with azoospermia or oligozoospermia due to single gene mutation (Limited), mode of inheritance: YL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NLGN4Y gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLGN4Y 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				3 clinvar	1 clinvar	4
missense			2 clinvar			2
nonsense			1 clinvar			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	3	1

Variants in NLGN4Y

This is a list of pathogenic ClinVar variants found in the NLGN4Y region.

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

Position	Significance	ClinVar
Y-14622379-G-A	Uncertain significance (Jun 21, 2018)	559565
Y-14824201-C-T	Benign (Jun 07, 2017)	777318
Y-14829869-T-C	Likely benign (Aug 01, 2023)	2661891
Y-14830121-C-A	Uncertain significance (Jan 06, 2017)	391879
Y-14840423-C-T	Uncertain significance (Feb 23, 2022)	2689591
Y-14840785-C-T	Likely benign (Aug 04, 2017)	770316
Y-14840887-C-T	Likely benign (Apr 01, 2023)	2661892

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLGN4Y	protein_coding	protein_coding	ENST00000355905	5	323013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0994	0.870	67952	5	0	67957	0.0000368

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	118	170	0.694	0.0000287	5409
Missense in Polyphen		59	101	0.58413		2988
Synonymous	-0.986	92	80.7	1.14	0.0000148	1612
Loss of Function	1.85	3	8.98	0.334	0.00000142	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000420
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000631	0.0000314
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Putative neuronal cell surface protein involved in cell- cell-interactions.;
Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses (Consensus)

Haploinsufficiency Scores

pHI: 0.233
hipred: N
hipred_score: 0.247
ghis: 0.497

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.181

Gene Damage Prediction

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

Gene ontology

Biological process: neuron cell-cell adhesion;learning;social behavior;synaptic vesicle endocytosis;modulation of chemical synaptic transmission;vocalization behavior;postsynaptic membrane assembly;presynaptic membrane assembly;presynapse assembly
Cellular component: plasma membrane;integral component of plasma membrane;cell surface;postsynaptic density;cell junction;synapse;postsynaptic membrane;spanning component of membrane;presynapse;symmetric, GABA-ergic, inhibitory synapse;asymmetric, glutamatergic, excitatory synapse
Molecular function: protein binding;signaling receptor activity;neurexin family protein binding;cell adhesion molecule binding;scaffold protein binding