RTL3

retrotransposon Gag like 3, the group of Retrotransposon Gag like|Zinc fingers CCHC-type

Basic information

Region (hg38): X:78656068-78659328

Previous symbols: [ "ZCCHC5" ]

Links

ENSG00000179300 ∙ NCBI:203430 ∙ ∙ HGNC:22997 ∙ Uniprot:Q8N8U3 ∙ 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 RTL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTL3 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			25	3		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	3	0

Variants in RTL3

This is a list of pathogenic ClinVar variants found in the RTL3 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-78657003-G-A		not specified	Uncertain significance (Apr 17, 2023)
X-78657018-G-A			Likely benign (Nov 01, 2022)
X-78657051-T-G		not specified	Uncertain significance (Nov 27, 2023)
X-78657126-C-T		not specified	Uncertain significance (May 16, 2024)
X-78657127-T-C		not specified	Uncertain significance (Oct 06, 2021)
X-78657144-A-G		not specified	Uncertain significance (Apr 07, 2022)
X-78657145-T-C		not specified	Uncertain significance (Sep 01, 2021)
X-78657159-G-A		not specified	Uncertain significance (Jul 11, 2023)
X-78657195-C-T		not specified	Uncertain significance (Jun 23, 2023)
X-78657269-A-T		not specified	Uncertain significance (Jul 28, 2021)
X-78657325-C-A		not specified	Likely benign (Dec 19, 2023)
X-78657381-G-A		not specified	Uncertain significance (Mar 18, 2024)
X-78657436-T-C		not specified	Uncertain significance (Mar 07, 2023)
X-78657465-G-T		not specified	Uncertain significance (Apr 18, 2023)
X-78657508-A-G		not specified	Uncertain significance (Apr 11, 2023)
X-78657661-A-G		not specified	Uncertain significance (Nov 19, 2022)
X-78657699-G-C		not specified	Uncertain significance (Mar 24, 2023)
X-78657714-A-G		not specified	Uncertain significance (Apr 20, 2024)
X-78657726-T-G		not specified	Uncertain significance (Feb 07, 2023)
X-78657727-C-G		not specified	Uncertain significance (Aug 04, 2023)
X-78657801-T-C		not specified	Uncertain significance (Oct 26, 2022)
X-78657850-G-T		not specified	Uncertain significance (Jun 18, 2024)
X-78657889-C-T		not specified	Likely benign (May 14, 2024)
X-78657904-A-G		not specified	Uncertain significance (Dec 07, 2021)
X-78657915-T-C		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTL3	protein_coding	protein_coding	ENST00000321110	1	3260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.40e-11	0.0150	125614	36	87	125737	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.93	227	159	1.43	0.0000107	3094
Missense in Polyphen		21	16.11	1.3035		410
Synonymous	-1.86	81	62.3	1.30	0.00000418	941
Loss of Function	-0.919	14	10.7	1.30	7.52e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00137	0.00122
Ashkenazi Jewish	0.00101	0.000695
East Asian	0.00198	0.00147
Finnish	0.000255	0.000185
European (Non-Finnish)	0.000679	0.000466
Middle Eastern	0.00198	0.00147
South Asian	0.000222	0.000131
Other	0.000222	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a transcriptional regulator. Plays a role in postnatal myogenesis, may be involved in the regulation of satellite cells self-renewal. {ECO:0000250|UniProtKB:Q6P1Y1}.

Intolerance Scores

• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.46

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Rtl3

Gene ontology

• Cellular component: nucleus
• Molecular function: nucleic acid binding;zinc ion binding