RAET1G

retinoic acid early transcript 1G

Basic information

Region (hg38): 6:149916878-149923121

Links

ENSG00000203722 ∙ NCBI:353091 ∙ OMIM:609244 ∙ HGNC:16795 ∙ Uniprot:Q6H3X3 ∙ 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 RAET1G gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAET1G 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in RAET1G

This is a list of pathogenic ClinVar variants found in the RAET1G region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149918238-G-A		not specified	Uncertain significance (Mar 22, 2024)
6-149918306-A-G		not specified	Uncertain significance (May 30, 2022)
6-149919075-C-T		not specified	Uncertain significance (Jan 23, 2024)
6-149919139-T-C		not specified	Uncertain significance (Dec 02, 2021)
6-149919142-T-C		not specified	Likely benign (Mar 01, 2023)
6-149919204-A-G		not specified	Uncertain significance (Jan 23, 2023)
6-149919240-C-T		not specified	Uncertain significance (Dec 17, 2021)
6-149919268-T-A		not specified	Uncertain significance (Dec 05, 2023)
6-149919271-C-T		not specified	Likely benign (May 04, 2023)
6-149919288-T-C		not specified	Uncertain significance (Sep 14, 2022)
6-149919319-G-C		not specified	Uncertain significance (Apr 01, 2024)
6-149919564-T-C		not specified	Uncertain significance (Aug 10, 2021)
6-149919585-A-C		not specified	Uncertain significance (Dec 19, 2023)
6-149919601-G-A		not specified	Uncertain significance (Jan 19, 2024)
6-149919610-C-G		not specified	Uncertain significance (Dec 08, 2023)
6-149919676-G-T		not specified	Uncertain significance (Apr 04, 2024)
6-149919801-C-G		not specified	Uncertain significance (Jun 07, 2023)
6-149922935-C-T		not specified	Uncertain significance (Apr 01, 2024)
6-149922962-G-T		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAET1G	protein_coding	protein_coding	ENST00000367360	5	6244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000682	0.493	125735	0	6	125741	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.325	189	177	1.07	0.00000944	2150
Missense in Polyphen		43	46.806	0.91868		665
Synonymous	-1.73	88	69.6	1.26	0.00000421	673
Loss of Function	0.639	9	11.3	0.795	4.92e-7	135

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	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: Binds and activates the KLRK1/NKG2D receptor, mediating natural killer cell cytotoxicity. {ECO:0000269|PubMed:15240696, ECO:0000269|PubMed:18544572, ECO:0000269|PubMed:19658097}.; FUNCTION: Isoform 2: Stimulates natural killer cells to secrete IFNG. {ECO:0000269|PubMed:18544572}.
• 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: 0.0540

Intolerance Scores

• loftool: 0.707
• rvis_EVS: 1.91
• rvis_percentile_EVS: 97.38

Haploinsufficiency Scores

• pHI: 0.0765
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0455

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;positive regulation of natural killer cell cytokine production;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;integral component of membrane;anchored component of membrane
• Molecular function: protein binding;natural killer cell lectin-like receptor binding