NSG2

neuronal vesicle trafficking associated 2

Basic information

Region (hg38): 5:174045706-174243501

Links

ENSG00000170091 ∙ NCBI:51617 ∙ OMIM:616752 ∙ HGNC:24955 ∙ Uniprot:Q9Y328 ∙ 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 NSG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSG2 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in NSG2

This is a list of pathogenic ClinVar variants found in the NSG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-174046772-G-C		not specified	Uncertain significance (Mar 21, 2023)
5-174046783-G-A		not specified	Uncertain significance (Dec 06, 2021)
5-174046814-A-T		not specified	Uncertain significance (Apr 23, 2024)
5-174046859-A-T		not specified	Uncertain significance (Jan 26, 2022)
5-174064263-C-A		not specified	Uncertain significance (Jun 05, 2023)
5-174064314-C-T		not specified	Uncertain significance (Jan 10, 2023)
5-174107432-G-A		not specified	Uncertain significance (Nov 17, 2022)
5-174107477-C-A		not specified	Uncertain significance (Nov 28, 2023)
5-174107483-C-T		not specified	Uncertain significance (Sep 27, 2022)
5-174107485-C-A		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSG2	protein_coding	protein_coding	ENST00000303177	4	197898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.884	0.115	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.660	87	106	0.820	0.00000649	1103
Missense in Polyphen		31	36.316	0.85362		390
Synonymous	-0.457	48	44.1	1.09	0.00000286	339
Loss of Function	2.45	0	7.00	0.00	2.94e-7	93

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.491
• ghis: 0.540

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nsg2

Gene ontology

• Biological process: dopamine receptor signaling pathway;endosomal transport;clathrin coat assembly
• Cellular component: endosome;early endosome;late endosome;Golgi apparatus;integral component of membrane;dendrite;cytoplasmic vesicle membrane;early endosome membrane;multivesicular body membrane;trans-Golgi network membrane;lysosomal lumen;Golgi cis cisterna membrane
• Molecular function: clathrin light chain binding