ISM2

isthmin 2, the group of Isthmin family

Basic information

Region (hg38): 14:77474394-77498816

Previous symbols: [ "THSD3" ]

Links

ENSG00000100593 ∙ NCBI:145501 ∙ OMIM:612684 ∙ HGNC:23176 ∙ Uniprot:Q6H9L7 ∙ 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 ISM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ISM2 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			59	4	2	65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	59	4	2

Variants in ISM2

This is a list of pathogenic ClinVar variants found in the ISM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-77475599-T-C		not specified	Uncertain significance (Dec 02, 2024)
14-77475633-C-T		not specified	Uncertain significance (Apr 06, 2024)
14-77475641-A-G		not specified	Likely benign (Jul 30, 2024)
14-77475666-C-T		not specified	Uncertain significance (Jan 26, 2022)
14-77475671-T-C		not specified	Uncertain significance (Oct 19, 2024)
14-77475696-G-A		not specified	Uncertain significance (Apr 14, 2022)
14-77475698-C-T		not specified	Uncertain significance (Feb 12, 2025)
14-77475789-C-T		not specified	Uncertain significance (Jun 29, 2023)
14-77475803-C-T		not specified	Uncertain significance (Mar 01, 2023)
14-77475816-G-A		not specified	Uncertain significance (May 22, 2024)
14-77475846-C-T		not specified	Uncertain significance (Sep 17, 2021)
14-77475894-G-A		not specified	Uncertain significance (Feb 10, 2022)
14-77475927-G-C		not specified	Uncertain significance (Jan 26, 2023)
14-77475929-G-A		not specified	Uncertain significance (May 17, 2023)
14-77475951-G-A		not specified	Uncertain significance (Aug 09, 2021)
14-77475959-C-A		not specified	Uncertain significance (Nov 08, 2022)
14-77475959-C-T		not specified	Uncertain significance (Jan 12, 2024)
14-77475960-G-A		not specified	Uncertain significance (Aug 08, 2023)
14-77475972-C-T		not specified	Uncertain significance (Mar 20, 2024)
14-77476041-G-A		not specified	Uncertain significance (Jul 12, 2023)
14-77476074-C-T		not specified	Uncertain significance (Sep 17, 2021)
14-77478265-T-C		not specified	Uncertain significance (Mar 31, 2024)
14-77478268-C-T		not specified	Likely benign (May 23, 2023)
14-77478284-A-G		not specified	Uncertain significance (Sep 27, 2021)
14-77478306-G-A		not specified	Likely benign (Nov 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ISM2	protein_coding	protein_coding	ENST00000342219	7	24471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.33e-11	0.246	125632	0	115	125747	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.346	307	325	0.946	0.0000189	3660
Missense in Polyphen		91	97.922	0.92931		907
Synonymous	-0.320	143	138	1.03	0.00000848	1144
Loss of Function	0.881	19	23.6	0.804	0.00000111	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000269	0.000267
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000933	0.0000924
European (Non-Finnish)	0.000849	0.000835
Middle Eastern	0.0000545	0.0000544
South Asian	0.000230	0.000229
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.770
• rvis_EVS: 0.34
• rvis_percentile_EVS: 73.7

Haploinsufficiency Scores

• pHI: 0.0807
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.115

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ism2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Cellular component: extracellular region