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

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

not_specified (138 variants)
not_provided (40 variants)
IQCE-related_disorder (22 variants)
Polydactyly,_postaxial,_type_a7 (13 variants)
Polydactyly,_postaxial,_type_A1 (2 variants)
Syndactyly (1 variants)
Retinal_degeneration (1 variants)
Inborn_genetic_diseases (1 variants)
Brachydactyly (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. These statistics are base on transcript: NM_000152558.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				13 clinvar	13 clinvar	26
missense			126 clinvar	15 clinvar	9 clinvar	150
nonsense	1 clinvar	2 clinvar	1 clinvar			4
start loss		1				1
frameshift	3 clinvar	3 clinvar	2 clinvar			8
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar	1 clinvar			3
Total	5	7	130	28	22

Highest pathogenic variant AF is 0.0014473789

Loading clinvar variants...

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