DELEC1

deleted in esophageal cancer 1, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 9:114850968-115402644

Previous symbols: [ "DEC1" ]

Links

ENSG00000173077 ∙ NCBI:50514 ∙ OMIM:604767 ∙ HGNC:23658 ∙ Uniprot:Q9P2X7 ∙ 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 DELEC1 gene.

• not provided (234 variants)
• Inborn genetic diseases (93 variants)
• Autosomal dominant nonsyndromic hearing loss 56 (67 variants)
• not specified (9 variants)
• Hearing impairment (6 variants)
• TNC-related condition (4 variants)
• Progressive sensorineural hearing impairment;Myopia;Vertigo (1 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DELEC1 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1	1	113	105	125	345
Total	1	1	113	105	125

Variants in DELEC1

This is a list of pathogenic ClinVar variants found in the DELEC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-114904001-T-C		not specified	Uncertain significance (May 20, 2024)
9-114904080-C-T		not specified	Likely benign (Feb 10, 2022)
9-114904136-T-C		not specified	Uncertain significance (Mar 21, 2023)
9-114904137-G-C		not specified	Likely benign (Aug 02, 2023)
9-114904179-T-C		not specified	Uncertain significance (Oct 25, 2023)
9-114918105-G-A		not specified	Uncertain significance (Sep 25, 2023)
9-114930180-T-C		not specified	Uncertain significance (Aug 08, 2023)
9-114930210-C-T		not specified	Uncertain significance (Oct 06, 2021)
9-114930219-T-C		not specified	Uncertain significance (Dec 27, 2023)
9-114930279-G-C		not specified	Uncertain significance (Nov 13, 2023)
9-115021162-C-A		not specified	Uncertain significance (Sep 27, 2021)
9-115021170-C-T		TNC-related disorder	Likely benign (May 23, 2019)
9-115021171-G-A		not specified	Uncertain significance (Jan 07, 2021)
9-115021236-T-C		Autosomal dominant nonsyndromic hearing loss 56 • TNC-related disorder	Uncertain significance (Apr 08, 2022)
9-115021264-C-T		Autosomal dominant nonsyndromic hearing loss 56	Benign/Likely benign (Mar 15, 2022)
9-115021272-TA-T			Benign (Dec 06, 2018)
9-115021283-AAG-A			Likely benign (Aug 13, 2019)
9-115021284-AG-A		Autosomal dominant nonsyndromic hearing loss 56	Uncertain significance (Mar 23, 2020)
9-115023974-T-C		Autosomal dominant nonsyndromic hearing loss 56 • not specified	Uncertain significance (Oct 16, 2023)
9-115023986-T-C		Autosomal dominant nonsyndromic hearing loss 56	Benign (Mar 15, 2022)
9-115024229-G-A			Benign (Dec 10, 2018)
9-115026578-T-G		not specified	Uncertain significance (Jun 05, 2024)
9-115026592-G-A		TNC-related disorder	Likely benign (May 05, 2021)
9-115026630-G-T		not specified	Uncertain significance (Jan 29, 2024)
9-115026635-C-T		not specified • TNC-related disorder	Likely benign (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DELEC1	protein_coding	protein_coding	ENST00000374016	4	260827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000267	0.187	125647	0	93	125740	0.000370

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.126	35	37.2	0.942	0.00000167	452
Missense in Polyphen		12	9.4816	1.2656		112
Synonymous	-0.519	15	12.7	1.19	6.27e-7	130
Loss of Function	-0.741	6	4.33	1.38	1.84e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000370	0.000369
Ashkenazi Jewish	0.00	0.00
East Asian	0.00457	0.00458
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.00457	0.00458
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Candidate tumor suppressor. {ECO:0000269|PubMed:10612805}.
• Pathway: Circadian rhythm pathway (Consensus)

Intolerance Scores

• loftool: 0.730
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.45

Haploinsufficiency Scores

• pHI: 0.0348
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00391

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of cell population proliferation