RAET1L

retinoic acid early transcript 1L

Basic information

Region (hg38): 6:150018334-150025532

Links

ENSG00000155918 ∙ NCBI:154064 ∙ OMIM:611047 ∙ HGNC:16798 ∙ Uniprot:Q5VY80 ∙ 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 RAET1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAET1L 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			15	2	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	2

Variants in RAET1L

This is a list of pathogenic ClinVar variants found in the RAET1L region.

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

Position	Type	Phenotype	Significance	ClinVar
6-150020182-A-G		not specified	Uncertain significance (Jan 19, 2024)
6-150020200-G-A		not specified	Uncertain significance (Apr 20, 2024)
6-150020233-A-G		not specified	Likely benign (Oct 28, 2024)
6-150020917-G-T		not specified	Uncertain significance (Dec 20, 2023)
6-150020961-C-T		not specified	Uncertain significance (Aug 10, 2024)
6-150020964-A-G		not specified	Likely benign (Jan 18, 2022)
6-150020983-T-G		not specified	Uncertain significance (Mar 29, 2024)
6-150020997-A-T		not specified	Uncertain significance (Dec 21, 2023)
6-150021006-T-A		not specified	Uncertain significance (Oct 05, 2023)
6-150021037-T-G		not specified	Uncertain significance (Dec 10, 2024)
6-150021076-C-T		not specified	Uncertain significance (Jan 04, 2022)
6-150021094-A-G		not specified	Uncertain significance (Jun 19, 2024)
6-150021103-C-T		not specified	Uncertain significance (Jun 07, 2024)
6-150021136-G-A		not specified	Uncertain significance (May 17, 2023)
6-150021145-C-T		not specified	Uncertain significance (Dec 16, 2022)
6-150021167-T-G			Benign (Jul 05, 2018)
6-150021174-A-G			Benign (May 31, 2018)
6-150021175-G-C		not specified	Uncertain significance (Jan 06, 2023)
6-150021177-G-A		not specified	Uncertain significance (Jul 29, 2022)
6-150022010-C-T		not specified	Uncertain significance (Jul 12, 2023)
6-150022045-C-G		not specified	Uncertain significance (Dec 04, 2024)
6-150022171-T-G		not specified	Uncertain significance (May 23, 2023)
6-150022187-G-A		not specified	Likely benign (Jun 03, 2022)
6-150022216-G-T		not specified	Uncertain significance (Jun 22, 2023)
6-150025388-G-C		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAET1L	protein_coding	protein_coding	ENST00000367341	4	7199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.48e-10	0.0215	125725	0	12	125737	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.991	151	120	1.25	0.00000603	1584
Missense in Polyphen		22	19.505	1.1279		311
Synonymous	0.522	41	45.5	0.902	0.00000243	481
Loss of Function	-0.879	13	10.0	1.30	4.72e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000398	0.000398
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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:19658097, ECO:0000269|PubMed:28559451}.
• Pathway: Natural killer cell mediated cytotoxicity - Homo sapiens (human);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.0706

Intolerance Scores

• loftool: 0.930
• rvis_EVS: 2.84
• rvis_percentile_EVS: 99.11

Haploinsufficiency Scores

• pHI: 0.0901
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0543

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;viral process;natural killer cell activation;natural killer cell mediated cytotoxicity;susceptibility to natural killer cell mediated cytotoxicity
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum;plasma membrane;external side of plasma membrane;anchored component of membrane
• Molecular function: protein binding;natural killer cell lectin-like receptor binding