IQCN

IQ motif containing N

Basic information

Region (hg38): 19:18257097-18274500

Previous symbols: [ "KIAA1683" ]

Links

ENSG00000130518 ∙ NCBI:80726 ∙ OMIM:620160 ∙ HGNC:29350 ∙ Uniprot:Q9H0B3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 78	AR	General	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	Genitourinary	36321563

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IQCN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQCN 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				3		3
missense			101	27		128
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	101	30	0

Variants in IQCN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-18257185-T-C		not specified	Likely benign (May 26, 2024)
19-18257205-C-T		not specified	Likely benign (Dec 21, 2021)
19-18257241-G-A		not specified	Uncertain significance (Nov 17, 2022)
19-18257263-T-G		not specified	Uncertain significance (Dec 27, 2022)
19-18257307-G-A		not specified	Uncertain significance (Jan 31, 2022)
19-18257359-A-G		not specified	Uncertain significance (Apr 29, 2024)
19-18257388-C-T		not specified	Likely benign (Nov 09, 2021)
19-18257391-T-C		not specified	Likely benign (Apr 27, 2022)
19-18257436-C-A		not specified	Uncertain significance (Sep 01, 2021)
19-18257503-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-18257524-G-A		not specified	Uncertain significance (May 28, 2023)
19-18257559-G-A		not specified	Uncertain significance (Aug 22, 2023)
19-18257602-C-T		not specified	Uncertain significance (Apr 24, 2024)
19-18257628-C-T		not specified	Uncertain significance (Jun 13, 2023)
19-18257689-C-T		not specified	Likely benign (May 01, 2024)
19-18257723-G-T		not specified	Uncertain significance (Oct 24, 2023)
19-18257742-C-T			Likely benign (Jan 01, 2023)
19-18257773-G-T		not specified	Uncertain significance (Feb 17, 2024)
19-18257793-G-A		not specified	Uncertain significance (Nov 08, 2022)
19-18257796-G-T		not specified	Uncertain significance (Sep 01, 2021)
19-18257823-C-T		not specified	Uncertain significance (Feb 16, 2023)
19-18257824-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-18257824-G-C		not specified	Uncertain significance (May 26, 2023)
19-18257827-G-A		not specified	Uncertain significance (Mar 29, 2023)
19-18257832-C-T		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IQCN	protein_coding	protein_coding	ENST00000392413	3	17412

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-8	0.955	125589	0	159	125748	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.341	836	864	0.967	0.0000564	8687
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000924	0.000921
Ashkenazi Jewish	0.00	0.00
East Asian	0.000928	0.000925
Finnish	0.000178	0.000139
European (Non-Finnish)	0.000806	0.000747
Middle Eastern	0.000928	0.000925
South Asian	0.000850	0.000850
Other	0.000496	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0804

Intolerance Scores

• rvis_EVS: 3.76
• rvis_percentile_EVS: 99.61

Haploinsufficiency Scores

• pHI: 0.0792
• hipred: N
• hipred_score: 0.169
• ghis: 0.421

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Iqcn

Gene ontology

• Cellular component: nucleus;mitochondrion
• Molecular function: protein binding