RTL9

retrotransposon Gag like 9, the group of Retrotransposon Gag like

Basic information

Region (hg38): X:110358848-110456334

Previous symbols: [ "RGAG1" ]

Links

ENSG00000243978 ∙ NCBI:57529 ∙ OMIM:300965 ∙ HGNC:29245 ∙ Uniprot:Q8NET4 ∙ 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 RTL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTL9 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				2		2
missense			65	4		69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	65	6	0

Variants in RTL9

This is a list of pathogenic ClinVar variants found in the RTL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-110450700-T-C		not specified	Uncertain significance (Apr 05, 2023)
X-110450715-C-A		not specified	Uncertain significance (May 23, 2024)
X-110450737-G-C		not specified	Uncertain significance (Jan 26, 2023)
X-110450837-A-T		not specified	Uncertain significance (Apr 24, 2024)
X-110450862-C-G		not specified	Uncertain significance (Apr 01, 2024)
X-110450937-C-T		not specified	Uncertain significance (Jan 26, 2023)
X-110451046-G-T		not specified	Uncertain significance (May 21, 2024)
X-110451209-C-G			Likely benign (-)
X-110451240-T-C		not specified	Conflicting classifications of pathogenicity (Feb 01, 2023)
X-110451252-A-G		not specified	Uncertain significance (Jun 22, 2024)
X-110451505-C-G			Likely benign (Feb 01, 2023)
X-110451507-C-T		not specified	Uncertain significance (May 26, 2024)
X-110451531-G-A		not specified	Uncertain significance (Dec 28, 2022)
X-110451543-C-T		not specified	Uncertain significance (Dec 27, 2023)
X-110451585-C-T		not specified	Uncertain significance (Aug 30, 2021)
X-110451597-T-C		not specified	Uncertain significance (Dec 22, 2023)
X-110451616-G-A		not specified	Uncertain significance (Mar 29, 2022)
X-110451627-C-G		not specified	Uncertain significance (Jan 30, 2024)
X-110451635-G-T		not specified	Uncertain significance (Sep 19, 2022)
X-110451651-C-A		not specified	Uncertain significance (Nov 09, 2022)
X-110451704-A-T		not specified	Uncertain significance (May 16, 2023)
X-110451764-G-C		not specified	Likely benign (Sep 14, 2022)
X-110451780-C-T		not specified	Likely benign (Oct 05, 2023)
X-110451798-C-G		not specified	Uncertain significance (May 12, 2024)
X-110451803-G-A		not specified	Uncertain significance (Jan 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTL9	protein_coding	protein_coding	ENST00000465301	2	97519

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00269	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.669	568	525	1.08	0.0000379	8890
Missense in Polyphen		108	139.98	0.77155		2685
Synonymous	-0.286	202	197	1.03	0.0000155	3108
Loss of Function	4.13	1	21.8	0.0459	0.00000162	447

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

Intolerance Scores

• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.64

Haploinsufficiency Scores

• pHI: 0.184
• hipred: N
• hipred_score: 0.316

Mouse Genome Informatics

• Gene name: Rtl9