YTHDF3

YTH N6-methyladenosine RNA binding protein F3, the group of YTH domain containing N6-methyladenosine readers

Basic information

Region (hg38): 8:63168552-63212786

Links

ENSG00000185728 ∙ NCBI:253943 ∙ OMIM:618669 ∙ HGNC:26465 ∙ Uniprot:Q7Z739 ∙ 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 YTHDF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YTHDF3 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YTHDF3	protein_coding	protein_coding	ENST00000539294	5	44235

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00296	124706	0	3	124709	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	180	312	0.576	0.0000156	3848
Missense in Polyphen		29	79.434	0.36508		1033
Synonymous	-0.353	114	109	1.04	0.00000543	1137
Loss of Function	4.10	1	21.5	0.0465	9.19e-7	263

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000689	0.0000645
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs and promotes RNA translation efficiency (PubMed:28106072, PubMed:28106076, PubMed:28281539). M6A is a modification present at internal sites of mRNAs and some non- coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability (PubMed:22575960, PubMed:24284625, PubMed:28106072, PubMed:28106076, PubMed:28281539). Shares m6A- containing mRNAs targets with YTHDF1 and YTHDF2, and regulates different processes depending on the context (PubMed:28106072, PubMed:28106076). Facilitates the translation of targeted mRNAs in cooperation with YTHDF1 by binding to m6A-containing mRNAs and interacting with 40S and 60S ribosome subunits (PubMed:28106072, PubMed:28106076). Can also act as a regulator of mRNA stability in cooperation with YTHDF2 by binding to m6A-containing mRNA and promoting their degradation (PubMed:28106072). Recognizes and binds m6A-containing circular RNAs (circRNAs) and promotes their translation (PubMed:28281539). circRNAs are generated through back-splicing of pre-mRNAs, a non-canonical splicing process promoted by dsRNA structures across circularizing exons (PubMed:28281539). {ECO:0000269|PubMed:22575960, ECO:0000269|PubMed:24284625, ECO:0000269|PubMed:28106072, ECO:0000269|PubMed:28106076, ECO:0000269|PubMed:28281539}.

Haploinsufficiency Scores

• pHI: 0.365
• hipred: Y
• hipred_score: 0.673

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.352

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ythdf3

Gene ontology

• Biological process: positive regulation of translation;positive regulation of translational initiation;mRNA destabilization
• Cellular component: cytosol
• Molecular function: RNA binding;protein binding;ribosome binding;N6-methyladenosine-containing RNA binding