IQCE

IQ motif containing E

Basic information

Region (hg38): 7:2558972-2614733

Links

ENSG00000106012 ∙ NCBI:23288 ∙ OMIM:617631 ∙ HGNC:29171 ∙ Uniprot:Q6IPM2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• postaxial polydactyly type A (Supportive), mode of inheritance: AR
• polydactyly, postaxial, type a7 (Limited), mode of inheritance: AR
• polydactyly, postaxial, type a7 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Postaxial polydactyly, type A7	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	Musculoskeletal	28488682

ClinVar

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

• Polydactyly, postaxial, type a7 (1 variants)
• not provided (1 variants)
• Polydactyly, postaxial, type A1 (1 variants)
• Brachydactyly;Syndactyly;Retinal degeneration;Polydactyly, postaxial, type A1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQCE 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				10	16	26
missense			58	10	16	84
nonsense		1	1			2
start loss		1				1
frameshift	1	2				3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1		2	4	7
non coding				1	6	7
Total	1	4	59	21	38

Highest pathogenic variant AF is 0.00117

Variants in IQCE

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

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

Position	Type	Phenotype	Significance	ClinVar
7-2559180-C-T		IQCE-related disorder	Likely benign (Feb 23, 2019)
7-2559184-G-A		Polydactyly, postaxial, type a7	Likely pathogenic (Jun 03, 2020)
7-2567143-T-C		not specified	Uncertain significance (Jun 21, 2021)
7-2568994-C-T		not specified	Uncertain significance (Oct 26, 2022)
7-2571607-G-A		Polydactyly, postaxial, type a7	Benign (Aug 19, 2021)
7-2571622-C-T		not specified	Uncertain significance (Apr 15, 2024)
7-2571644-C-T			Likely benign (Jan 01, 2023)
7-2572204-A-T		not specified	Uncertain significance (Feb 27, 2024)
7-2572233-C-A			Benign (Dec 31, 2019)
7-2572244-T-C		Polydactyly, postaxial, type a7 • IQCE-related disorder	Benign (Aug 19, 2021)
7-2572248-G-A		not specified	Uncertain significance (Feb 27, 2023)
7-2572254-G-A		not specified	Likely benign (Feb 17, 2022)
7-2572256-C-T			Benign (Dec 31, 2019)
7-2572257-G-A		not specified	Likely benign (Jun 21, 2022)
7-2572268-C-G		not specified	Uncertain significance (May 31, 2024)
7-2572274-G-C			Benign (Jan 03, 2019)
7-2572288-G-A		IQCE-related disorder • not specified	Uncertain significance (Sep 27, 2021)
7-2572297-G-A		not specified	Uncertain significance (Jun 19, 2024)
7-2572312-G-A		not specified	Uncertain significance (Apr 04, 2024)
7-2572320-A-G		not specified	Uncertain significance (Sep 29, 2022)
7-2573408-G-C		Polydactyly, postaxial, type a7 • IQCE-related disorder	Benign (Aug 19, 2021)
7-2573417-G-A		Polydactyly, postaxial, type a7	Pathogenic (Sep 10, 2020)
7-2573427-C-A		not specified	Uncertain significance (Mar 07, 2024)
7-2573428-T-C		Polydactyly, postaxial, type a7 • IQCE-related disorder	Benign (Aug 19, 2021)
7-2573455-A-C		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IQCE	protein_coding	protein_coding	ENST00000402050	22	55737

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.38e-39	3.06e-8	124180	2	672	124854	0.00270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.934	480	426	1.13	0.0000273	4456
Missense in Polyphen		130	124.06	1.0479		1393
Synonymous	-1.61	209	181	1.15	0.0000129	1385
Loss of Function	-1.53	53	42.2	1.25	0.00000225	481

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00364	0.00363
Ashkenazi Jewish	0.00746	0.00717
East Asian	0.00186	0.00184
Finnish	0.00196	0.00190
European (Non-Finnish)	0.00323	0.00319
Middle Eastern	0.00186	0.00184
South Asian	0.00150	0.00147
Other	0.00200	0.00198

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the EvC complex that positively regulates ciliary Hedgehog (Hh) signaling. {ECO:0000250|UniProtKB:Q6PCQ0}.
• Pathway: Signal Transduction;Activation of SMO;Hedgehog ,on, state;Signaling by Hedgehog (Consensus)

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.996
• rvis_EVS: 1.41
• rvis_percentile_EVS: 94.82

Haploinsufficiency Scores

• pHI: 0.334
• hipred: N
• hipred_score: 0.123
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.144

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Iqce
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; limbs/digits/tail phenotype; vision/eye phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: limb morphogenesis
• Cellular component: cilium;ciliary membrane
• Molecular function: protein binding