EVC

EvC ciliary complex subunit 1

Basic information

Region (hg38): 4:5711201-5814305

Links

ENSG00000072840

∙ NCBI:2121 ∙ OMIM:604831 ∙ HGNC:3497 ∙ Uniprot:P57679 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Ellis-van Creveld syndrome (Definitive), mode of inheritance: AR
acrofacial dysostosis, Weyers type (Definitive), mode of inheritance: AR
Ellis-van Creveld syndrome (Supportive), mode of inheritance: AR
acrofacial dysostosis, Weyers type (Supportive), mode of inheritance: AD
Ellis-van Creveld syndrome (Strong), mode of inheritance: AR
acrofacial dysostosis, Weyers type (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ellis-van Creveld syndrome	AR	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Dental; Dermatologic; Musculoskeletal	7628126; 10700184; 17024374; 18454448; 18947413; 19744229; 20184732; 23220543

ClinVar

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

Ellis-van_Creveld_syndrome (1565 variants)
Curry-Hall_syndrome (1358 variants)
not_provided (221 variants)
Inborn_genetic_diseases (181 variants)
not_specified (98 variants)
EVC-related_disorder (56 variants)
Short-rib_thoracic_dysplasia_6_with_or_without_polydactyly (4 variants)
Nephronophthisis (1 variants)
EVC-associated_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EVC gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153717.3. 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		1 clinvar	19 clinvar	544 clinvar	4 clinvar	568
missense	2 clinvar	10 clinvar	374 clinvar	72 clinvar	12 clinvar	470
nonsense	51 clinvar	30 clinvar	1 clinvar			82
start loss	2	4				6
frameshift	80 clinvar	66 clinvar	8 clinvar			154
splice donor/acceptor (+/-2bp)	9 clinvar	49 clinvar				58
Total	144	160	402	616	16

Highest pathogenic variant AF is 0.0000532874

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EVC	protein_coding	protein_coding	ENST00000382674	21	117849

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.46e-25	0.0133	125639	0	109	125748	0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.25	598	518	1.16	0.0000341	6398
Missense in Polyphen		157	130.02	1.2075		1653
Synonymous	-2.42	278	231	1.20	0.0000168	1979
Loss of Function	1.17	43	52.1	0.825	0.00000265	598

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000769	0.000767
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000513	0.000510
Middle Eastern	0.000382	0.000381
South Asian	0.000360	0.000359
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the EvC complex that positively regulates ciliary Hedgehog (Hh) signaling. Involved in endochondral growth and skeletal development. {ECO:0000250|UniProtKB:P57680}.;
Disease: DISEASE: Acrofacial dysostosis, Weyers type (WAD) [MIM:193530]: An autosomal dominant condition characterized by dysplastic nails, postaxial polydactyly, dental anomalies, short limbs, short stature and normal intelligence. The phenotype is milder than Ellis-van Creveld syndrome. {ECO:0000269|PubMed:10700184}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Hedgehog signaling pathway - Homo sapiens (human);Hedgehog Signaling Pathway;Signal Transduction;Activation of SMO;Hedgehog ,on, state;Signaling by Hedgehog (Consensus)

Recessive Scores

pRec: 0.180

Intolerance Scores

loftool: 0.832
rvis_EVS: 3.73
rvis_percentile_EVS: 99.58

Haploinsufficiency Scores

pHI: 0.127
hipred: N
hipred_score: 0.270
ghis: 0.434

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.157

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Evc
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype; craniofacial phenotype; growth/size/body region phenotype; cellular phenotype;

Gene ontology

Biological process: skeletal system development;endochondral bone growth;smoothened signaling pathway;muscle organ development;positive regulation of smoothened signaling pathway;cartilage development
Cellular component: cytoplasm;cilium;integral component of membrane;ciliary basal body;ciliary membrane;plasma membrane protein complex
Molecular function