IQCE

protein-coding

IQ motif containing E

Gene summary

Involved in limb morphogenesis. Predicted to be located in cytoplasmic side of plasma membrane. Predicted to be part of plasma membrane protein complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152558.5

Inheritance

ClinVar variants

P:14U:167B:61

Top phenotype

Postaxial polydactyly, type A7

gnomAD constraint

pLI —, LoF o/e 1.25

Max pathogenic AF

—

Genomic locus

chr7:2,558,972-2,614,733

External References & Databases

Ensembl (ENSG00000106012)

Transcript & Mutation Effects

hg38 • Region Span ~55.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

postaxial polydactyly type ASUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019673

Submitter: Orphanet

polydactyly, postaxial, type a7LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0060550

Submitter: Laboratory for Molecular Medicine

This gene-disease relationship has undergone rapid assessment. Classifications are based on preliminary review of gene-disease validity during analysis of genomic sequencing results.

polydactyly, postaxial, type a7STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0060550

Submitter: PanelApp Australia

polydactyly, postaxial, type a7LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0060550

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Postaxial polydactyly, type A7AR

Manifestation: Musculoskeletal

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: 28488682

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IQCE variants in ClinVar

9 Conditions Cataloged

not specifiedTotal: 174

not providedTotal: 47

IQCE-related disorderTotal: 30

Polydactyly, postaxial, type a7Total: 14

Polydactyly, postaxial, type A1Total: 2

SyndactylyTotal: 1

Retinal degenerationTotal: 1

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152558.5. 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			2 clinvar	22 clinvar	11 clinvar	35
missense			150 clinvar	18 clinvar	10 clinvar	178
nonsense	2 clinvar	2 clinvar	1 clinvar			5
start loss		1 clinvar				1
frameshift	2 clinvar	3 clinvar	3 clinvar			8
splice donor/acceptor (+/-2bp)	1 clinvar	3 clinvar	11 clinvar			15
Total	5	9	167	40	21	242

Highest pathogenic variant AF is 0.0014473789

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152558.5	RefSeq	NP_689771.3	22	MANE Select
ENST00000402050.7	Ensembl	ENSP00000385597.2	22	MANE Select
NM_001287499.2	RefSeq	NP_001274428.1	21	Standard
NM_001287500.2	RefSeq	NP_001274429.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Activation of SMO
Hedgehog ,on, state
Signaling by Hedgehog

Biological Process

limb morphogenesis

Molecular Function

protein binding

Cellular Component

cilium
ciliary membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000402050
Coding exons: 22
Length: 55737
Individuals with no LoFs: 124180
Homozygous LoFs: 2
Heterozygous LoFs: 672
Defined: 124854
p: 0.00270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.934	480	426	1.13	0.0000273	4456
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00078	0.00077	rare
Latino/Admixed American	0.0029	0.0028	notable
Ashkenazi Jewish	0.0075	0.0072	notable
East Asian	0.0019	0.0018	notable
Finnish	0.0020	0.0019	notable
European (Non-Finnish)	0.0032	0.0032	notable
South Asian	0.0015	0.0015	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the EvC complex that positively regulates ciliary Hedgehog (Hh) signaling. {ECO:0000250|UniProtKB:Q6PCQ0}.;

Recessive Scores

pRec: 0.0998

Intolerance Scores

LoFtool: 0.996
RVIS EVS: 1.41
RVIS percentile EVS: 94.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.144

Gene Damage Prediction

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