RTL5

retrotransposon Gag like 5, the group of Retrotransposon Gag like

Basic information

Region (hg38): X:72127109-72131915

Previous symbols: [ "RGAG4" ]

Links

ENSG00000242732 ∙ NCBI:340526 ∙ ∙ HGNC:29430 ∙ Uniprot:Q5HYW3 ∙ 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 RTL5 gene.

• Inborn genetic diseases (8 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTL5 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
missense			8	3	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	4	1

Variants in RTL5

This is a list of pathogenic ClinVar variants found in the RTL5 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-72129877-G-A		not specified	Uncertain significance (Apr 06, 2024)
X-72129887-G-A		not specified	Conflicting classifications of pathogenicity (Dec 06, 2023)
X-72129904-C-T		not specified	Uncertain significance (Dec 26, 2023)
X-72129941-G-A			Likely benign (Mar 01, 2023)
X-72129943-C-T		not specified	Uncertain significance (Jan 29, 2024)
X-72129958-G-C		not specified	Uncertain significance (Nov 08, 2022)
X-72130009-C-T		not specified	Uncertain significance (Aug 02, 2022)
X-72130073-C-G		not specified	Uncertain significance (Oct 13, 2023)
X-72130112-C-G		not specified	Uncertain significance (Oct 04, 2022)
X-72130112-C-T		not specified	Likely benign (Jun 01, 2023)
X-72130205-C-T		not specified	Uncertain significance (May 23, 2024)
X-72130277-C-G		not specified	Uncertain significance (Aug 26, 2022)
X-72130282-C-T		not specified	Likely benign (Jan 04, 2024)
X-72130283-T-G			Benign (Sep 25, 2021)
X-72130288-C-A		not specified	Uncertain significance (Aug 02, 2023)
X-72130373-T-C		not specified	Likely benign (Jun 17, 2024)
X-72130403-C-T		not specified	Uncertain significance (Jan 23, 2024)
X-72130447-C-G		not specified	Uncertain significance (Sep 20, 2023)
X-72130490-C-G		not specified	Uncertain significance (May 07, 2024)
X-72130540-T-C		not specified	Uncertain significance (Dec 08, 2023)
X-72130606-C-G		not specified	Uncertain significance (Jun 30, 2022)
X-72130614-T-A		not specified	Uncertain significance (May 06, 2022)
X-72130745-A-C		not specified	Uncertain significance (Jun 29, 2023)
X-72130787-C-T			Uncertain significance (Nov 01, 2022)
X-72130817-G-C		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTL5	protein_coding	protein_coding	ENST00000545866	1	4801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000186	0.905	124607	22	30	124659	0.000209

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.203	230	239	0.963	0.0000191	3714
Missense in Polyphen		53	71.979	0.73633		1153
Synonymous	0.0499	96	96.6	0.994	0.00000747	1140
Loss of Function	1.51	8	14.1	0.566	0.00000125	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.000960
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000807	0.0000556
Finnish	0.0000654	0.0000464
European (Non-Finnish)	0.000213	0.000150
Middle Eastern	0.0000807	0.0000556
South Asian	0.000545	0.000294
Other	0.000228	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.153
• ghis: 0.551

Mouse Genome Informatics

• Gene name: Rtl5