IQSEC3

IQ motif and Sec7 domain ArfGEF 3, the group of IQSEC ArfGEF family

Basic information

Region (hg38): 12:66767-178455

Links

ENSG00000120645 ∙ NCBI:440073 ∙ OMIM:612118 ∙ HGNC:29193 ∙ Uniprot:Q9UPP2 ∙ 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 IQSEC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQSEC3 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	7		8
missense			64	4	3	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	2	3
Total	0	0	65	12	5

Variants in IQSEC3

This is a list of pathogenic ClinVar variants found in the IQSEC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-66923-A-G			Benign (Jul 22, 2018)
12-66992-A-G		not specified	Uncertain significance (Oct 29, 2021)
12-67084-C-T		not specified	Uncertain significance (Nov 09, 2021)
12-67167-G-A			Likely benign (Oct 01, 2022)
12-67206-G-A			Likely benign (May 31, 2018)
12-67212-T-C			Likely benign (Jan 03, 2019)
12-99148-A-G		not specified	Uncertain significance (Dec 27, 2023)
12-99156-G-A		not specified	Uncertain significance (Aug 30, 2021)
12-99157-T-C		not specified	Uncertain significance (Sep 23, 2023)
12-99183-G-A		not specified	Uncertain significance (Feb 16, 2023)
12-99198-G-A		not specified	Uncertain significance (Dec 19, 2022)
12-125692-C-T		not specified	Uncertain significance (Oct 12, 2022)
12-125703-G-A		not specified	Uncertain significance (Mar 31, 2024)
12-125716-C-T		not specified	Uncertain significance (Oct 26, 2021)
12-125725-C-T		not specified	Uncertain significance (Oct 26, 2021)
12-125731-C-T		not specified	Uncertain significance (Aug 30, 2022)
12-125737-C-G		not specified	Uncertain significance (May 26, 2022)
12-125767-C-G		not specified	Uncertain significance (Sep 02, 2024)
12-125767-C-T		not specified	Uncertain significance (Jun 30, 2023)
12-125781-G-A		not specified	Uncertain significance (Sep 30, 2024)
12-125785-C-T		not specified	Uncertain significance (Dec 28, 2022)
12-125796-G-A			Benign (Oct 01, 2022)
12-125815-C-T		not specified	Uncertain significance (Oct 27, 2022)
12-125820-G-A		not specified	Uncertain significance (Apr 07, 2023)
12-125823-C-T		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IQSEC3	protein_coding	protein_coding	ENST00000538872	14	111696

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00387	0.996	122177	48	3523	125748	0.0143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	597	682	0.876	0.0000433	7398
Missense in Polyphen		186	279.36	0.6658		2908
Synonymous	-0.728	348	331	1.05	0.0000243	2434
Loss of Function	4.33	13	44.0	0.295	0.00000221	494

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0148	0.0148
Ashkenazi Jewish	0.00915	0.00917
East Asian	0.000109	0.000109
Finnish	0.0317	0.0312
European (Non-Finnish)	0.0197	0.0196
Middle Eastern	0.000109	0.000109
South Asian	0.00490	0.00488
Other	0.0159	0.0158

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a guanine nucleotide exchange factor (GEF) for ARF1. {ECO:0000269|PubMed:17981261}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.350
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.4

Haploinsufficiency Scores

• pHI: 0.526
• hipred: Y
• hipred_score: 0.735
• ghis: 0.617

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.246

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Iqsec3
• Phenotype: skeleton phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: actin cytoskeleton organization;regulation of ARF protein signal transduction
• Cellular component: cytoplasm;postsynaptic density;cell junction;postsynaptic membrane;inhibitory synapse;glycinergic synapse;GABA-ergic synapse;postsynaptic specialization of symmetric synapse
• Molecular function: ARF guanyl-nucleotide exchange factor activity