RELCH

RAB11 binding and LisH domain, coiled-coil and HEAT repeat containing, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 18:62187255-62310249

Previous symbols: [ "KIAA1468" ]

Links

ENSG00000134444 ∙ NCBI:57614 ∙ OMIM:618001 ∙ HGNC:29289 ∙ Uniprot:Q9P260 ∙ 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 RELCH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RELCH 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	2
missense			48		1	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	48	2	2

Variants in RELCH

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

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

Position	Type	Phenotype	Significance	ClinVar
18-62187536-A-C		not specified	Uncertain significance (Aug 31, 2022)
18-62187537-G-A		not specified	Uncertain significance (May 10, 2024)
18-62187546-G-C		not specified	Uncertain significance (Dec 10, 2024)
18-62187574-T-A		not specified	Uncertain significance (Jun 18, 2021)
18-62187578-G-A		not specified	Uncertain significance (Aug 08, 2022)
18-62187660-C-G		not specified	Uncertain significance (Feb 13, 2024)
18-62187708-G-A		not specified	Uncertain significance (Jun 06, 2023)
18-62187725-G-A		not specified	Uncertain significance (Oct 24, 2024)
18-62187732-C-T		not specified	Uncertain significance (Jan 22, 2024)
18-62187752-G-A		not specified	Uncertain significance (Dec 17, 2023)
18-62187768-C-A		not specified	Uncertain significance (Sep 11, 2024)
18-62187773-G-A		not specified	Uncertain significance (Jan 26, 2022)
18-62187792-C-G		not specified	Uncertain significance (Oct 09, 2024)
18-62187939-C-T		not specified	Uncertain significance (Jun 18, 2024)
18-62187945-T-C		not specified	Uncertain significance (Oct 25, 2023)
18-62187974-G-T		not specified	Uncertain significance (Apr 11, 2023)
18-62211156-G-A		not specified	Uncertain significance (Jul 07, 2022)
18-62211185-T-G		not specified	Uncertain significance (Oct 03, 2022)
18-62221228-T-G		not specified	Uncertain significance (Mar 21, 2023)
18-62221243-G-A		not specified	Uncertain significance (Jan 18, 2022)
18-62221396-C-A		not specified	Uncertain significance (Sep 30, 2024)
18-62227333-T-G			Likely benign (Jun 01, 2018)
18-62227363-T-G		not specified	Uncertain significance (Jun 29, 2023)
18-62227365-G-T		not specified	Uncertain significance (Feb 23, 2023)
18-62227374-A-G		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RELCH	protein_coding	protein_coding	ENST00000398130	29	119865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000651	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.87	361	636	0.568	0.0000315	7867
Missense in Polyphen		99	243.97	0.4058		3003
Synonymous	1.82	200	236	0.849	0.0000117	2387
Loss of Function	6.57	9	67.0	0.134	0.00000359	823

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000926	0.0000926
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.00	0.00
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000626	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates intracellular cholesterol distribution from recycling endosomes to the trans-Golgi network through interactions with RAB11 and OSBP (PubMed:29514919). Functions in membrane tethering and promotes OSBP-mediated cholesterol transfer between RAB11-bound recycling endosomes and OSBP-bound Golgi-like membranes (PubMed:29514919). {ECO:0000269|PubMed:29514919}.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: -1.29
• rvis_percentile_EVS: 5.08

Haploinsufficiency Scores

• pHI: 0.182
• hipred: Y
• hipred_score: 0.673
• ghis: 0.589

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Relch

Gene ontology

• Biological process: intracellular cholesterol transport
• Cellular component: trans-Golgi network;recycling endosome