IQCH

protein-coding

IQ motif containing H

Gene summary

Predicted to act upstream of or within lncRNA transcription and single fertilization. Predicted to be active in nuclear speck. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001031715.3

Inheritance

—

ClinVar variants

P:2U:138B:22

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr15:67,254,786-67,502,260

External References & Databases

Ensembl (ENSG00000103599)

Transcript & Mutation Effects

hg38 • Region Span ~247.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IQCH variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 145

not providedTotal: 8

Primary ciliary dyskinesiaTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031715.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	2 clinvar	2 clinvar	8
missense			133 clinvar	18 clinvar		151
nonsense		1 clinvar				1
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	1	138	20	2	162

Highest pathogenic variant AF is 0.00019516825

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031715.3	RefSeq	NP_001026885.2	21	MANE Select
ENST00000335894.9	Ensembl	ENSP00000336861.4	21	MANE Select
NM_001284347.2	RefSeq	NP_001271276.2	12	Standard
NM_001284348.2	RefSeq	NP_001271277.2	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335894
Coding exons: 21
Length: 247461
Individuals with no LoFs: 125366
Homozygous LoFs: 2
Heterozygous LoFs: 380
Defined: 125748
p: 0.00152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.772	505	556	0.908	0.0000287	6755
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0029	0.0028	notable
Latino/Admixed American	0.0012	0.0012	notable
Ashkenazi Jewish	0.0015	0.0015	notable
East Asian	0.0049	0.0048	notable
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00090	0.00090	rare
South Asian	0.0028	0.0027	notable
Other	0.0011	0.0011	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.353

Gene Damage Prediction

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