DERL3

derlin 3, the group of Rhomboid family

Basic information

Region (hg38): 22:23834503-23839128

Previous symbols: [ "C22orf14" ]

Links

ENSG00000099958 ∙ NCBI:91319 ∙ OMIM:610305 ∙ HGNC:14236 ∙ Uniprot:Q96Q80 ∙ 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 DERL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DERL3 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				1		1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				2	1	3
Total	0	0	12	3	1

Variants in DERL3

This is a list of pathogenic ClinVar variants found in the DERL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-23834542-T-G			Likely benign (Jan 02, 2019)
22-23836864-G-A			Likely benign (May 01, 2024)
22-23836979-G-A			Benign (May 01, 2022)
22-23837076-G-C		not specified	Uncertain significance (Oct 06, 2022)
22-23837116-C-T		not specified	Uncertain significance (Jan 26, 2022)
22-23837147-C-T			Likely benign (Nov 01, 2023)
22-23837705-C-T		not specified	Uncertain significance (Nov 08, 2022)
22-23837757-T-C		not specified	Uncertain significance (Aug 09, 2021)
22-23837803-T-C		not specified	Uncertain significance (Nov 09, 2021)
22-23837830-A-C		not specified	Uncertain significance (Mar 18, 2024)
22-23838363-C-A		not specified	Uncertain significance (Mar 31, 2023)
22-23838363-C-T		not specified	Uncertain significance (Aug 18, 2023)
22-23838431-C-G		not specified	Uncertain significance (Apr 23, 2024)
22-23838571-G-C		not specified	Uncertain significance (Oct 29, 2021)
22-23838576-T-A		not specified	Uncertain significance (May 30, 2024)
22-23838585-A-C		not specified	Uncertain significance (Dec 13, 2022)
22-23838588-C-A		not specified	Uncertain significance (Apr 05, 2023)
22-23838591-A-C		not specified	Uncertain significance (Jun 17, 2022)
22-23838610-A-C		not specified	Uncertain significance (Apr 08, 2023)
22-23838723-G-C		not specified	Uncertain significance (Mar 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DERL3	protein_coding	protein_coding	ENST00000406855	7	4626

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000219	0.758	125276	0	399	125675	0.00159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.166	148	142	1.04	0.00000812	1520
Missense in Polyphen		45	36.357	1.2377		385
Synonymous	-0.920	70	60.9	1.15	0.00000364	481
Loss of Function	1.03	7	10.6	0.659	5.26e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00286	0.00283
Ashkenazi Jewish	0.00559	0.00537
East Asian	0.000119	0.000109
Finnish	0.00191	0.00185
European (Non-Finnish)	0.00173	0.00161
Middle Eastern	0.000119	0.000109
South Asian	0.000617	0.000588
Other	0.00190	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functional component of endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal glycoproteins, but not that of misfolded nonglycoproteins. May act by forming a channel that allows the retrotranslocation of misfolded glycoproteins into the cytosol where they are ubiquitinated and degraded by the proteasome. May mediate the interaction between VCP and the misfolded glycoproteins (PubMed:16449189, PubMed:22607976). May be involved in endoplasmic reticulum stress-induced pre-emptive quality control, a mechanism that selectively attenuates the translocation of newly synthesized proteins into the endoplasmic reticulum and reroutes them to the cytosol for proteasomal degradation (PubMed:26565908). {ECO:0000269|PubMed:16449189, ECO:0000269|PubMed:22607976, ECO:0000269|PubMed:26565908}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Disorders of transmembrane transporters;Disease;Defective CFTR causes cystic fibrosis;Transport of small molecules;ABC-family proteins mediated transport;ABC transporter disorders (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.906
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.233
• hipred: Y
• hipred_score: 0.626
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.927

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Derl3
• Phenotype: normal phenotype

Gene ontology

• Biological process: protein N-linked glycosylation via asparagine;ubiquitin-dependent ERAD pathway;endoplasmic reticulum unfolded protein response;negative regulation of retrograde protein transport, ER to cytosol
• Cellular component: signal recognition particle receptor complex;integral component of endoplasmic reticulum membrane;signal recognition particle
• Molecular function: protein binding