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.

• not_specified (77 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000152694.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			70	7		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	70	7	0

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