RELT

RELT TNF receptor, the group of Tumor necrosis factor receptor superfamily|RELT family

Basic information

Region (hg38): 11:73376399-73397474

Previous symbols: [ "TNFRSF19L" ]

Links

ENSG00000054967 ∙ NCBI:84957 ∙ OMIM:611211 ∙ HGNC:13764 ∙ Uniprot:Q969Z4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
• amelogenesis imperfecta type 1 (Supportive), mode of inheritance: AD
• amelogenesis imperfecta, type 3C (Moderate), mode of inheritance: AR
• amelogenesis imperfecta, type 3C (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amelogenesis imperfecta, type IIIC	AR	General	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	Dental	30506946

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RELT 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				2	4	6
missense		2	28	4	3	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	2	28	6	7

Variants in RELT

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

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

Position	Type	Phenotype	Significance	ClinVar
11-73389158-C-T		Inborn genetic diseases	Likely benign (Jun 05, 2024)
11-73389159-G-A		Inborn genetic diseases	Uncertain significance (Jun 06, 2022)
11-73390541-GTTC-G			Likely benign (Dec 01, 2022)
11-73390557-C-T		Inborn genetic diseases	Uncertain significance (Nov 30, 2021)
11-73390558-C-G		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)
11-73390558-C-T		Inborn genetic diseases	Uncertain significance (Jan 20, 2023)
11-73390584-A-G		Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
11-73390587-A-C		Inborn genetic diseases	Uncertain significance (Feb 03, 2022)
11-73390620-G-C		Inborn genetic diseases	Uncertain significance (Mar 29, 2022)
11-73390626-G-T			Likely pathogenic (Aug 27, 2021)
11-73390753-A-G		Amelogenesis imperfecta, type 3C	Pathogenic (Apr 11, 2019)
11-73390798-C-T		Amelogenesis imperfecta, type 3C	Pathogenic (Oct 01, 2019)
11-73390843-G-T		Inborn genetic diseases	Uncertain significance (Oct 03, 2023)
11-73390866-G-A		Inborn genetic diseases	Uncertain significance (Mar 31, 2023)
11-73390894-A-T		Amelogenesis imperfecta	Likely pathogenic (May 20, 2023)
11-73392250-C-T		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
11-73392258-A-T		Inborn genetic diseases	Uncertain significance (Sep 16, 2022)
11-73392264-G-A		Inborn genetic diseases	Uncertain significance (Aug 15, 2023)
11-73392283-C-T		Inborn genetic diseases	Uncertain significance (Jan 22, 2024)
11-73392323-C-T		RELT-related disorder	Likely benign (Jun 01, 2022)
11-73392334-C-T		Inborn genetic diseases	Uncertain significance (Dec 14, 2023)
11-73392357-T-C		Inborn genetic diseases	Uncertain significance (Nov 30, 2022)
11-73392364-T-G		Amelogenesis imperfecta	Likely pathogenic (May 20, 2023)
11-73392405-C-T		Inborn genetic diseases	Uncertain significance (Jan 10, 2023)
11-73392406-G-A		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RELT	protein_coding	protein_coding	ENST00000064780	10	21211

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000107	0.941	125670	0	78	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.275	287	274	1.05	0.0000179	2714
Missense in Polyphen		95	99.433	0.95541		988
Synonymous	-0.675	124	115	1.08	0.00000770	933
Loss of Function	1.82	13	22.3	0.583	0.00000109	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000861	0.000860
Ashkenazi Jewish	0.00	0.00
East Asian	0.00169	0.00169
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.00169	0.00169
South Asian	0.000165	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in apoptosis (PubMed:28688764, PubMed:19969290). Induces activation of MAPK14/p38 and MAPK8/JNK MAPK cascades, when overexpressed (PubMed:16530727). {ECO:0000269|PubMed:16530727, ECO:0000269|PubMed:19969290, ECO:0000269|PubMed:28688764}.
• Pathway: Cytokine-cytokine receptor interaction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.763
• rvis_EVS: 0
• rvis_percentile_EVS: 54.03

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.131
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Relt

Gene ontology

• Biological process: apoptotic process
• Cellular component: nucleus;plasma membrane;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: protein binding