ISM1

isthmin 1, the group of Isthmin family

Basic information

Region (hg38): 20:13221273-13300651

Previous symbols: [ "C20orf82" ]

Links

ENSG00000101230 ∙ NCBI:140862 ∙ OMIM:615793 ∙ HGNC:16213 ∙ Uniprot:B1AKI9 ∙ 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 ISM1 gene.

• Inborn genetic diseases (23 variants)
• ISM1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ISM1 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			21	2		23
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in ISM1

This is a list of pathogenic ClinVar variants found in the ISM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-13221790-C-T		ISM1-related disorder	Uncertain significance (Feb 02, 2024)
20-13221796-AGCT-A		ISM1-related disorder	Likely benign (Feb 14, 2022)
20-13221798-C-G		not specified	Uncertain significance (Nov 08, 2022)
20-13221855-T-C		not specified	Uncertain significance (Aug 22, 2023)
20-13270532-C-T		not specified	Uncertain significance (Sep 26, 2022)
20-13270580-T-C		not specified	Likely benign (Oct 12, 2022)
20-13270617-G-A		ISM1-related disorder	Likely benign (Dec 24, 2021)
20-13270624-C-T		ISM1-related disorder	Uncertain significance (Oct 03, 2023)
20-13270640-A-G		not specified	Uncertain significance (Nov 12, 2021)
20-13270678-C-T		ISM1-related disorder	Likely benign (Apr 26, 2023)
20-13270741-C-G		ISM1-related disorder	Benign (Oct 07, 2019)
20-13279652-G-A		ISM1-related disorder	Benign (Nov 14, 2019)
20-13279655-G-A		not specified	Uncertain significance (Aug 04, 2021)
20-13279680-A-T		not specified	Uncertain significance (Jun 29, 2023)
20-13279689-C-T		not specified	Uncertain significance (Oct 03, 2022)
20-13279724-G-A		not specified	Uncertain significance (Nov 20, 2023)
20-13279762-C-G		ISM1-related disorder	Likely benign (Apr 22, 2019)
20-13279811-G-A		not specified	Uncertain significance (Sep 27, 2021)
20-13279847-C-T		not specified	Uncertain significance (Jun 29, 2023)
20-13279866-G-A		not specified	Uncertain significance (Mar 28, 2023)
20-13279896-A-C		not specified	Uncertain significance (Jan 30, 2024)
20-13288549-A-G		not specified	Uncertain significance (Jul 25, 2023)
20-13288553-C-A		ISM1-related disorder	Likely benign (Apr 26, 2023)
20-13288586-C-T		ISM1-related disorder	Likely benign (Aug 27, 2019)
20-13288615-G-A		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ISM1	protein_coding	protein_coding	ENST00000262487	6	78881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00629	0.990	124605	0	35	124640	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	216	265	0.815	0.0000164	3040
Missense in Polyphen		63	112.83	0.55836		1285
Synonymous	0.297	110	114	0.965	0.00000836	894
Loss of Function	2.53	7	18.9	0.371	9.82e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000439	0.000439
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.000698	0.000696
European (Non-Finnish)	0.0000805	0.0000796
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an angiogenesis inhibitor. {ECO:0000250|UniProtKB:A2ATD1}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.619
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Haploinsufficiency Scores

• pHI: 0.341
• hipred: N
• hipred_score: 0.489
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ism1

Zebrafish Information Network

• Gene name: ism1
• Affected structure: neutrophil
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of angiogenesis
• Cellular component: extracellular region