RAET1E

retinoic acid early transcript 1E

Basic information

Region (hg38): 6:149883178-149898113

Links

ENSG00000164520 ∙ NCBI:135250 ∙ OMIM:609243 ∙ HGNC:16793 ∙ Uniprot:Q8TD07 ∙ 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 RAET1E gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAET1E 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in RAET1E

This is a list of pathogenic ClinVar variants found in the RAET1E region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149888548-A-C		not specified	Uncertain significance (May 10, 2023)
6-149888640-T-G		not specified	Uncertain significance (Dec 15, 2023)
6-149888652-G-A		not specified	Likely benign (Aug 02, 2022)
6-149889408-C-T		not specified	Uncertain significance (May 13, 2022)
6-149889432-A-T		not specified	Uncertain significance (Aug 04, 2023)
6-149889490-A-C		not specified	Uncertain significance (Dec 15, 2023)
6-149889505-C-T		not specified	Uncertain significance (Jul 17, 2023)
6-149889516-C-A		not specified	Uncertain significance (Nov 10, 2022)
6-149889542-T-C		not specified	Uncertain significance (Apr 08, 2022)
6-149889575-C-T		not specified	Uncertain significance (Jul 14, 2021)
6-149889576-G-A		not specified	Uncertain significance (Dec 11, 2023)
6-149889929-A-G		not specified	Uncertain significance (Dec 02, 2021)
6-149889971-C-A		not specified	Uncertain significance (Dec 17, 2023)
6-149889983-G-A		not specified	Uncertain significance (Oct 04, 2023)
6-149889984-C-A		not specified	Uncertain significance (Oct 04, 2023)
6-149890023-T-A		not specified	Uncertain significance (Jun 16, 2023)
6-149890868-G-A		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAET1E	protein_coding	protein_coding	ENST00000357183	4	14728

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-7	0.159	125631	0	7	125638	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0237	138	139	0.994	0.00000694	1710
Missense in Polyphen		18	20.669	0.87085		326
Synonymous	0.678	48	54.4	0.883	0.00000299	503
Loss of Function	-0.0875	10	9.71	1.03	5.01e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds and activates the KLRK1/NKG2D receptor, mediating natural killer cell cytotoxicity. {ECO:0000269|PubMed:15240696, ECO:0000269|PubMed:18544572}.
• Pathway: Natural killer cell mediated cytotoxicity - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.759
• rvis_EVS: 2.15
• rvis_percentile_EVS: 97.98

Haploinsufficiency Scores

• pHI: 0.0333
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00775

Gene Damage Prediction

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

Gene ontology

• Biological process: T cell mediated cytotoxicity;immune response;natural killer cell activation;natural killer cell mediated cytotoxicity;susceptibility to natural killer cell mediated cytotoxicity;positive regulation of natural killer cell mediated cytotoxicity;regulation of immune response
• Cellular component: extracellular region;extracellular space;plasma membrane;external side of plasma membrane;integral component of membrane
• Molecular function: protein binding;natural killer cell lectin-like receptor binding