RTL8C

retrotransposon Gag like 8C, the group of Retrotransposon Gag like

Basic information

Region (hg38): X:135032355-135033546

Previous symbols: [ "CXX1", "FAM127A" ]

Links

ENSG00000134590 ∙ NCBI:8933 ∙ OMIM:300213 ∙ HGNC:2569 ∙ Uniprot:A6ZKI3, O15255 ∙ 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 RTL8C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTL8C 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in RTL8C

This is a list of pathogenic ClinVar variants found in the RTL8C 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-135032567-G-A		not specified	Uncertain significance (May 23, 2023)
X-135032715-A-G		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTL8C	protein_coding	protein_coding	ENST00000257013	1	1244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.457	0.456	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	18	47.6	0.378	0.00000312	737
Missense in Polyphen		0	12.455	0		218
Synonymous	-0.509	25	22.0	1.14	0.00000148	237
Loss of Function	1.15	0	1.55	0.00	1.01e-7	21

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

Recessive Scores

• pRec: 0.0887

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

• pHI: 0.0408
• hipred: N
• hipred_score: 0.238
• ghis: 0.493

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Rtl8c

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;plasma membrane