INSM2

INSM transcriptional repressor 2, the group of SNAG transcriptional repressors|Zinc fingers C2H2-type

Basic information

Region (hg38): 14:35534164-35537054

Links

ENSG00000168348 ∙ NCBI:84684 ∙ OMIM:614027 ∙ HGNC:17539 ∙ Uniprot:Q96T92 ∙ 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 INSM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INSM2 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				1		1
missense			44	2		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	3	0

Variants in INSM2

This is a list of pathogenic ClinVar variants found in the INSM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-35534261-G-T		not specified	Uncertain significance (Nov 10, 2024)
14-35534294-C-T			Likely benign (Nov 01, 2024)
14-35534317-C-A		not specified	Uncertain significance (Dec 24, 2024)
14-35534322-C-T		not specified	Uncertain significance (Jul 09, 2021)
14-35534370-G-A		not specified	Uncertain significance (Sep 16, 2021)
14-35534419-C-A		not specified	Uncertain significance (May 01, 2022)
14-35534430-C-A		not specified	Uncertain significance (May 31, 2023)
14-35534461-G-A		not specified	Uncertain significance (Feb 27, 2024)
14-35534488-C-T		not specified	Uncertain significance (Feb 07, 2025)
14-35534505-G-C		not specified	Uncertain significance (Jun 17, 2022)
14-35534514-G-A		not specified	Uncertain significance (Feb 13, 2025)
14-35534535-C-T		not specified	Uncertain significance (Dec 20, 2023)
14-35534580-C-A		not specified	Uncertain significance (Nov 08, 2024)
14-35534583-A-T		not specified	Uncertain significance (Dec 14, 2021)
14-35534660-G-C		not specified	Uncertain significance (Jul 10, 2023)
14-35534704-C-T		not specified	Uncertain significance (Aug 12, 2021)
14-35534727-A-G		not specified	Uncertain significance (Feb 28, 2023)
14-35534731-C-T		not specified	Uncertain significance (May 08, 2023)
14-35534764-C-G		not specified	Uncertain significance (Dec 07, 2022)
14-35534829-C-G		not specified	Uncertain significance (Sep 16, 2021)
14-35534848-G-A		not specified	Uncertain significance (May 24, 2024)
14-35534857-A-G		not specified	Uncertain significance (Aug 17, 2022)
14-35534865-A-C		not specified	Likely benign (Aug 16, 2021)
14-35534872-G-A		not specified	Uncertain significance (Nov 17, 2023)
14-35534898-A-G		not specified	Likely benign (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INSM2	protein_coding	protein_coding	ENST00000307169	1	3013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.882	0.118	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.777	253	290	0.872	0.0000136	3507
Missense in Polyphen		87	110.85	0.78487		1292
Synonymous	0.111	133	135	0.988	0.00000651	1306
Loss of Function	2.85	1	11.3	0.0882	4.97e-7	142

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

• Function: FUNCTION: May function as a growth suppressor or tumor suppressor in liver cells and in certain neurons. {ECO:0000250}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.474
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• pHI: 0.156
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.492

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Insm2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding