IQCH

IQ motif containing H

Basic information

Region (hg38): 15:67254785-67502260

Links

ENSG00000103599 ∙ NCBI:64799 ∙ OMIM:612523 ∙ HGNC:25721 ∙ Uniprot:Q86VS3 ∙ 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 IQCH gene.

• Inborn genetic diseases (40 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQCH 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	2	3
missense			33	9		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	33	10	3

Variants in IQCH

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

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

Position	Type	Phenotype	Significance	ClinVar
15-67254917-C-T			Benign (Mar 29, 2018)
15-67254920-C-G		not specified	Uncertain significance (Dec 21, 2022)
15-67254924-C-T		not specified	Uncertain significance (Mar 11, 2022)
15-67254963-C-A			Benign (Nov 10, 2018)
15-67261332-G-A		not specified	Likely benign (May 26, 2022)
15-67261345-A-G		not specified	Uncertain significance (Jan 06, 2023)
15-67263126-A-G		not specified	Uncertain significance (Oct 13, 2023)
15-67263128-A-G		not specified	Uncertain significance (Jul 20, 2021)
15-67279399-C-T		not specified	Uncertain significance (Jan 29, 2024)
15-67279492-C-T		not specified	Uncertain significance (Feb 28, 2024)
15-67336975-A-G		not specified	Likely benign (Oct 26, 2022)
15-67337068-C-T		not specified	Uncertain significance (Sep 27, 2022)
15-67344108-G-A		not specified	Likely benign (Nov 18, 2022)
15-67344173-C-T		not specified	Uncertain significance (Aug 12, 2021)
15-67344185-A-G		not specified	Likely benign (Aug 02, 2023)
15-67359848-G-A		not specified	Uncertain significance (Sep 26, 2023)
15-67359857-G-A		not specified	Likely benign (Jan 25, 2023)
15-67372124-A-G		not specified	Uncertain significance (Jul 19, 2023)
15-67372130-C-T		not specified	Uncertain significance (Aug 02, 2023)
15-67372177-G-T		not specified	Uncertain significance (Oct 05, 2023)
15-67372236-A-T		not specified	Uncertain significance (Dec 01, 2022)
15-67372272-C-T			Benign (Nov 20, 2018)
15-67372367-T-C		not specified	Uncertain significance (Mar 16, 2022)
15-67372367-T-G		not specified	Uncertain significance (May 23, 2023)
15-67372375-T-G		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IQCH	protein_coding	protein_coding	ENST00000335894	21	247461

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-21	0.197	125366	2	380	125748	0.00152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.772	505	556	0.908	0.0000287	6755
Missense in Polyphen		167	206.18	0.80996		2585
Synonymous	1.25	186	209	0.890	0.0000115	1946
Loss of Function	1.68	40	53.2	0.752	0.00000265	643

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00409	0.00402
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.00489	0.00480
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000902	0.000897
Middle Eastern	0.00489	0.00480
South Asian	0.00276	0.00268
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a regulatory role in spermatogenesis. {ECO:0000269|PubMed:15897968}.

Intolerance Scores

• loftool: 0.631
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.84

Haploinsufficiency Scores

• pHI: 0.367
• hipred: N
• hipred_score: 0.169
• ghis: 0.385

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.353

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Iqch

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function