RTL1

retrotransposon Gag like 1, the group of Retrotransposon Gag like

Basic information

Region (hg38): 14:100879753-100903722

Links

ENSG00000254656 ∙ NCBI:388015 ∙ OMIM:611896 ∙ HGNC:14665 ∙ Uniprot:A6NKG5 ∙ 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 RTL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTL1 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				11	3	14
missense			67	10	3	80
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	67	21	6

Variants in RTL1

This is a list of pathogenic ClinVar variants found in the RTL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-100880774-G-T		not specified	Uncertain significance (Jul 26, 2022)
14-100880789-C-T		not specified	Uncertain significance (Mar 16, 2022)
14-100880806-C-T		not specified	Likely benign (Jan 11, 2023)
14-100880807-G-A		not specified	Uncertain significance (Dec 20, 2023)
14-100880906-G-A		not specified	Uncertain significance (Nov 10, 2022)
14-100880914-A-G		not specified	Uncertain significance (May 13, 2024)
14-100880947-C-T		not specified	Likely benign (Aug 10, 2021)
14-100880953-C-T		not specified	Uncertain significance (Feb 10, 2022)
14-100880959-G-C		not specified	Uncertain significance (May 31, 2023)
14-100880984-G-A		not specified	Uncertain significance (Sep 29, 2023)
14-100881018-C-T			Benign (Dec 31, 2019)
14-100881065-G-A		not specified	Uncertain significance (Aug 15, 2023)
14-100881111-A-G			Likely benign (Nov 26, 2018)
14-100881145-C-T			Benign/Likely benign (Oct 01, 2023)
14-100881146-G-A		not specified	Uncertain significance (Aug 11, 2022)
14-100881176-T-G		not specified	Uncertain significance (Jun 16, 2023)
14-100881189-G-A			Likely benign (Nov 01, 2022)
14-100881197-C-T		not specified	Uncertain significance (Mar 08, 2024)
14-100881228-C-T			Benign (Dec 31, 2019)
14-100881251-A-G		not specified	Likely benign (Aug 16, 2022)
14-100881254-G-A		not specified	Uncertain significance (Oct 26, 2021)
14-100881260-C-G		not specified	Uncertain significance (Dec 21, 2022)
14-100881265-C-T		not specified	Uncertain significance (Nov 09, 2021)
14-100881297-A-C			Likely benign (May 01, 2023)
14-100881332-C-T			Benign (Apr 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTL1	protein_coding	protein_coding	ENST00000534062	1	4193

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00561	0.994	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.69	629	850	0.740	0.0000549	8849
Missense in Polyphen		133	229.6	0.57927		2400
Synonymous	2.23	324	379	0.854	0.0000273	2785
Loss of Function	3.58	10	31.8	0.314	0.00000170	327

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface and for development of the placenta. {ECO:0000250}.

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.580
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.65

Haploinsufficiency Scores

• pHI: 0.229
• hipred: N
• hipred_score: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtl1
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: multicellular organism development
• Cellular component: integral component of membrane