RTL4

retrotransposon Gag like 4, the group of Retrotransposon Gag like|Zinc fingers CCHC-type

Basic information

Region (hg38): X:112083015-112457514

Previous symbols: [ "ZCCHC16" ]

Links

ENSG00000187823 ∙ NCBI:340595 ∙ ∙ HGNC:25214 ∙ Uniprot:Q6ZR62 ∙ 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 RTL4 gene.

• Inborn genetic diseases (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTL4 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			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in RTL4

This is a list of pathogenic ClinVar variants found in the RTL4 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-112454742-C-T		not specified	Uncertain significance (Oct 22, 2021)
X-112454804-C-T		not specified	Uncertain significance (Dec 15, 2023)
X-112454805-G-A		not specified	Likely benign (Aug 03, 2022)
X-112454900-C-T		not specified	Uncertain significance (Aug 30, 2021)
X-112454907-A-G		not specified	Uncertain significance (Dec 14, 2022)
X-112455021-T-C		not specified	Uncertain significance (Mar 07, 2024)
X-112455083-A-T		not specified	Uncertain significance (Sep 14, 2023)
X-112455177-C-T		not specified	Uncertain significance (Jan 17, 2023)
X-112455276-A-C		not specified	Uncertain significance (Feb 21, 2024)
X-112455280-C-A		not specified	Uncertain significance (Feb 23, 2023)
X-112455297-A-T		not specified	Uncertain significance (Dec 01, 2022)
X-112455384-A-G		not specified	Likely benign (Feb 10, 2022)
X-112455470-A-G		not specified	Uncertain significance (Feb 07, 2023)
X-112455546-G-A		not specified	Uncertain significance (Aug 26, 2022)
X-112455600-G-A		not specified	Conflicting classifications of pathogenicity (Sep 01, 2022)
X-112455601-A-T		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTL4	protein_coding	protein_coding	ENST00000340433	1	2747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000345	0.206	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.529	130	114	1.14	0.00000830	2044
Missense in Polyphen		27	21.057	1.2822		409
Synonymous	0.207	42	43.7	0.960	0.00000310	613
Loss of Function	-0.196	8	7.42	1.08	6.28e-7	107

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

• Function: FUNCTION: Involved in cognitive function in the brain, possibly via the noradrenergic system. {ECO:0000250|UniProtKB:Q3URY0}.

Recessive Scores

• pRec: 0.0804

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.112
• ghis: 0.386

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Rtl4
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: norepinephrine metabolic process;cognition
• Molecular function: nucleic acid binding;zinc ion binding