ISX

intestine specific homeobox, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 22:35066136-35087387

Links

ENSG00000175329 ∙ NCBI:91464 ∙ OMIM:612019 ∙ HGNC:28084 ∙ Uniprot:Q2M1V0 ∙ 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 ISX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ISX 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					2	2
missense			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	3

Variants in ISX

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

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

Position	Type	Phenotype	Significance	ClinVar
22-35067143-G-A		not specified	Uncertain significance (Mar 01, 2023)
22-35067191-C-T		not specified	Uncertain significance (Jul 05, 2022)
22-35067222-T-C			Benign (Apr 20, 2018)
22-35067238-G-A		not specified	Uncertain significance (Nov 02, 2023)
22-35067259-G-A		not specified	Uncertain significance (Mar 24, 2023)
22-35082557-C-T		not specified	Uncertain significance (Jun 24, 2022)
22-35082593-A-T		not specified	Uncertain significance (Jan 19, 2024)
22-35082599-C-T		not specified	Uncertain significance (Feb 06, 2024)
22-35082612-C-G		not specified	Uncertain significance (May 30, 2024)
22-35082613-G-C		not specified	Uncertain significance (Apr 12, 2022)
22-35082618-C-A		not specified	Uncertain significance (Jan 09, 2024)
22-35082623-G-A		not specified	Uncertain significance (Dec 31, 2023)
22-35082643-A-T		not specified	Uncertain significance (Apr 04, 2023)
22-35082651-C-T			Benign (Aug 20, 2018)
22-35082653-C-A		not specified	Uncertain significance (Mar 29, 2023)
22-35084413-C-T		not specified	Uncertain significance (Oct 10, 2023)
22-35084435-A-G		not specified	Likely benign (Oct 05, 2021)
22-35084444-C-T		not specified	Uncertain significance (Aug 22, 2023)
22-35084461-G-A		not specified	Uncertain significance (Dec 21, 2022)
22-35084497-G-A		not specified	Uncertain significance (Mar 28, 2024)
22-35085467-C-A		not specified	Uncertain significance (Dec 13, 2023)
22-35085490-G-A		not specified	Uncertain significance (May 06, 2024)
22-35085512-C-T		not specified	Uncertain significance (May 20, 2024)
22-35085571-G-A		not specified	Uncertain significance (Jul 30, 2023)
22-35085572-C-T		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ISX	protein_coding	protein_coding	ENST00000308700	4	21252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000356	0.381	125567	0	178	125745	0.000708

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.430	152	138	1.10	0.00000760	1565
Missense in Polyphen		46	38.36	1.1992		413
Synonymous	-0.480	60	55.5	1.08	0.00000312	506
Loss of Function	0.203	7	7.60	0.921	4.03e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.000101	0.0000924
European (Non-Finnish)	0.00111	0.00111
Middle Eastern	0.000599	0.000598
South Asian	0.0000654	0.0000653
Other	0.00163	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that regulates gene expression in intestine. May participate in vitamin A metabolism most likely by regulating BCO1 expression in the intestine (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• loftool: 0.229
• rvis_EVS: 1.26
• rvis_percentile_EVS: 93.56

Haploinsufficiency Scores

• pHI: 0.0955
• 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: 0.0936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Isx
• Phenotype: normal phenotype

Gene ontology

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