IQCN

protein-coding

IQ motif containing N

Gene summary

Involved in spermatid development. Located in mitochondrion. Implicated in spermatogenic failure 78. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA1683

MANE transcript

NM_001145304.2

Inheritance

ClinVar variants

P:8U:256B:58

Top phenotype

Spermatogenic failure 78

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr19:18,257,098-18,274,500

External References & Databases

Ensembl (ENSG00000130518)

Transcript & Mutation Effects

hg38 • Region Span ~17.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Spermatogenic failure 78AR

Manifestation: Genitourinary

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 36321563

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IQCN variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 302

Spermatogenic failure 78Total: 8

not providedTotal: 7

IQCN-related conditionTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145304.2. 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				8 clinvar		8
missense			255 clinvar	50 clinvar		305
nonsense		3 clinvar				3
start loss						0
frameshift	1 clinvar	4 clinvar				5
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	7	256	58	0	322

Highest pathogenic variant AF is 0.00056209037

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145304.2	RefSeq	NP_001138776.1	3	MANE Select
ENST00000392413.5	Ensembl	ENSP00000376213.2	3	MANE Select
NM_001145305.2	RefSeq	NP_001138777.1	2	Standard
NM_025249.4	RefSeq	NP_079525.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

nucleus
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392413
Coding exons: 3
Length: 17412
Individuals with no LoFs: 125589
Homozygous LoFs: 0
Heterozygous LoFs: 159
Defined: 125748
p: 0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.341	836	864	0.967	0.0000564	8687
Missense (PolyPhen)		140	172.27	0.81268		1790
Synonymous	-0.708	388	371	1.05	0.0000256	3065
Loss of Function	2.00	17	28.5	0.596	0.00000140	326

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00093	0.00092	rare
Finnish	0.00018	0.00014	rare
European (Non-Finnish)	0.00081	0.00075	rare
South Asian	0.00085	0.00085	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0804

Intolerance Scores

RVIS EVS: 3.76
RVIS percentile EVS: 99.61

Essentials

Essential (gene trap): N