DLEC1

DLEC1 cilia and flagella associated protein, the group of Cilia and flagella associated

Basic information

Region (hg38): 3:38039205-38124025

Links

ENSG00000008226 ∙ NCBI:9940 ∙ OMIM:604050 ∙ HGNC:2899 ∙ Uniprot:Q9Y238 ∙ 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 DLEC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DLEC1 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				6	6	12
missense			113	17	5	135
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			2			2
Total	0	0	115	23	11

Variants in DLEC1

This is a list of pathogenic ClinVar variants found in the DLEC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-38039238-A-G		not specified	Uncertain significance (Jun 14, 2024)
3-38039250-C-T		not specified	Uncertain significance (Jul 14, 2023)
3-38039269-G-A		not specified	Uncertain significance (Jul 11, 2023)
3-38039272-C-T			Likely benign (Aug 14, 2017)
3-38039275-A-G		not specified	Uncertain significance (Aug 22, 2023)
3-38039284-A-G		not specified	Uncertain significance (Dec 27, 2022)
3-38039299-C-T		not specified	Uncertain significance (Apr 20, 2024)
3-38039377-A-G			Likely benign (Aug 31, 2017)
3-38039451-G-A		not specified	Uncertain significance (Jan 17, 2024)
3-38039452-A-T		not specified	Uncertain significance (Jan 17, 2024)
3-38039475-C-T			Likely benign (May 01, 2023)
3-38039530-A-G		not specified	Uncertain significance (Aug 05, 2023)
3-38039580-A-G		not specified	Uncertain significance (Dec 18, 2023)
3-38039592-A-G		not specified	Uncertain significance (Dec 13, 2023)
3-38039620-T-C		not specified	Uncertain significance (Nov 27, 2023)
3-38045543-A-T		not specified	Uncertain significance (Jul 26, 2022)
3-38045547-G-A		not specified	Uncertain significance (Aug 22, 2023)
3-38045577-T-C		not specified	Uncertain significance (Jul 05, 2023)
3-38045592-G-A		not specified	Uncertain significance (Aug 14, 2023)
3-38045616-G-T		not specified	Uncertain significance (Jul 12, 2023)
3-38045637-G-A		not specified	Uncertain significance (Nov 09, 2023)
3-38045669-G-A		not specified	Uncertain significance (Dec 03, 2021)
3-38045674-C-T			Benign (Aug 11, 2018)
3-38059754-C-T			Benign (Apr 03, 2018)
3-38059757-G-A			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DLEC1	protein_coding	protein_coding	ENST00000308059	37	84821

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.13e-35	0.0848	123852	4	1022	124878	0.00412

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.499	1044	1.00e+3	1.04	0.0000560	11433
Missense in Polyphen		264	257.76	1.0242		2980
Synonymous	-0.656	422	405	1.04	0.0000233	3520
Loss of Function	2.26	67	90.1	0.744	0.00000465	997

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00469	0.00461
Ashkenazi Jewish	0.00335	0.00328
East Asian	0.000723	0.000723
Finnish	0.00167	0.00167
European (Non-Finnish)	0.00677	0.00674
Middle Eastern	0.000723	0.000723
South Asian	0.00167	0.00164
Other	0.00398	0.00379

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a tumor suppressor by inhibiting cell proliferation. {ECO:0000269|PubMed:10213508}.
• Disease: DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The gene represented in this entry may be involved in disease pathogenesis. DLEC1 silencing due to promoter methylation and aberrant transcription are implicated in the development of lung cancer.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. {ECO:0000269|PubMed:10213508}. Note=The gene represented in this entry may be involved in disease pathogenesis. DLEC1 silencing due to promoter methylation and aberrant transcription may be implicated in the development of esophageal cancer.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.935
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.93

Haploinsufficiency Scores

• pHI: 0.982
• hipred: N
• hipred_score: 0.233
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.112

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dlec1
• Phenotype: reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of cell population proliferation
• Cellular component: cytoplasm;cytosol
• Molecular function: molecular_function