INSYN2A

inhibitory synaptic factor 2A

Basic information

Region (hg38): 10:127135426-127196591

Previous symbols: [ "C10orf141", "FAM196A", "INSYN2" ]

Links

ENSG00000188916 ∙ NCBI:642938 ∙ OMIM:617129 ∙ HGNC:33859 ∙ Uniprot:Q6ZSG2 ∙ 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 INSYN2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INSYN2A 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			47	5		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	5	0

Variants in INSYN2A

This is a list of pathogenic ClinVar variants found in the INSYN2A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-127137863-C-T		not specified	Uncertain significance (Aug 13, 2021)
10-127137899-G-T		not specified	Uncertain significance (Jan 20, 2025)
10-127137932-A-G		not specified	Uncertain significance (Dec 28, 2024)
10-127137955-A-G		not specified	Uncertain significance (Jun 13, 2023)
10-127175327-C-T		not specified	Uncertain significance (Jan 04, 2022)
10-127175350-A-G		not specified	Uncertain significance (Sep 16, 2021)
10-127175377-A-G		not specified	Likely benign (Apr 27, 2022)
10-127175380-G-A		not specified	Uncertain significance (Jan 31, 2025)
10-127175440-C-T		not specified	Uncertain significance (Feb 07, 2025)
10-127175494-G-A		not specified	Uncertain significance (Oct 26, 2021)
10-127175510-C-T		not specified	Uncertain significance (Jan 02, 2025)
10-127175519-G-T		not specified	Uncertain significance (Mar 21, 2023)
10-127175528-T-C		not specified	Uncertain significance (Oct 25, 2023)
10-127175533-C-T		not specified	Likely benign (Jun 11, 2021)
10-127175534-G-A		not specified	Uncertain significance (Mar 25, 2024)
10-127175537-C-G		not specified	Uncertain significance (Dec 21, 2023)
10-127175542-T-A		not specified	Uncertain significance (Dec 15, 2024)
10-127175570-C-T		not specified	Uncertain significance (Oct 05, 2021)
10-127175600-G-A		not specified	Uncertain significance (Oct 08, 2024)
10-127175630-C-T		not specified	Uncertain significance (Apr 12, 2024)
10-127175698-C-T		not specified	Uncertain significance (Feb 28, 2024)
10-127175701-C-T		not specified	Uncertain significance (Oct 26, 2022)
10-127175702-G-A		not specified	Uncertain significance (Nov 24, 2024)
10-127175723-G-T		not specified	Uncertain significance (Dec 09, 2023)
10-127175735-C-A		not specified	Uncertain significance (Mar 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INSYN2A	protein_coding	protein_coding	ENST00000522781	3	60729

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.915	0.0851	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.121	308	302	1.02	0.0000196	3107
Missense in Polyphen		96	121.83	0.78796		1306
Synonymous	0.259	130	134	0.971	0.00000999	977
Loss of Function	3.34	2	16.7	0.120	8.15e-7	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000619	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000445	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the protein machinery at the inhibitory synapses, probably acting as a scaffold. Inhibitory synapses dampen neuronal activity through postsynaptic hyperpolarization. This synaptic inhibition is fundamental for the functioning of the central nervous system, shaping and orchestrating the flow of information through neuronal networks to generate a precise neural code. {ECO:0000250|UniProtKB:Q3USH1}.

Intolerance Scores

• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.6

Haploinsufficiency Scores

• pHI: 0.319
• hipred: Y
• hipred_score: 0.653
• ghis: 0.513

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Fam196a

Gene ontology

• Biological process: inhibitory postsynaptic potential
• Cellular component: postsynaptic density;cell junction;postsynaptic membrane