YTHDF1

YTH N6-methyladenosine RNA binding protein F1, the group of YTH domain containing N6-methyladenosine readers

Basic information

Region (hg38): 20:63195429-63216139

Previous symbols: [ "C20orf21" ]

Links

ENSG00000149658 ∙ NCBI:54915 ∙ OMIM:616529 ∙ HGNC:15867 ∙ Uniprot:Q9BYJ9 ∙ 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 YTHDF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YTHDF1 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				3	6	9
missense			38	2	1	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	5	7

Variants in YTHDF1

This is a list of pathogenic ClinVar variants found in the YTHDF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-63196721-C-T		not specified	Uncertain significance (Dec 20, 2021)
20-63202346-T-C		not specified	Uncertain significance (Oct 11, 2024)
20-63202358-G-T		not specified	Uncertain significance (Oct 13, 2023)
20-63202409-C-G		not specified	Uncertain significance (May 16, 2024)
20-63202446-G-T		not specified	Uncertain significance (Jun 16, 2024)
20-63202449-G-A			Benign (Jul 23, 2018)
20-63202482-A-G			Benign (Jun 05, 2018)
20-63202521-C-T			Benign (Jul 23, 2018)
20-63202646-C-T		not specified	Uncertain significance (Dec 03, 2024)
20-63202658-T-C		not specified	Uncertain significance (Oct 17, 2024)
20-63202717-T-C		not specified	Uncertain significance (Jun 07, 2024)
20-63202777-C-T		not specified	Uncertain significance (Jan 24, 2024)
20-63202802-T-C		not specified	Uncertain significance (Jul 29, 2022)
20-63202817-G-A			Benign (Apr 04, 2018)
20-63202859-T-C		not specified	Uncertain significance (Nov 10, 2024)
20-63202880-C-T		not specified	Uncertain significance (Jun 24, 2022)
20-63202886-C-T		not specified	Uncertain significance (Jul 16, 2024)
20-63202898-T-C		not specified	Uncertain significance (Sep 27, 2022)
20-63202917-G-A			Likely benign (Jul 01, 2022)
20-63202996-G-A		not specified	Likely benign (Nov 07, 2023)
20-63203011-G-C		not specified	Uncertain significance (Jun 26, 2024)
20-63203030-G-A		not specified	Uncertain significance (Jan 16, 2024)
20-63203035-G-C		not specified	Uncertain significance (Jan 04, 2022)
20-63203062-T-C		not specified	Uncertain significance (Jan 10, 2023)
20-63203098-G-A		not specified	Uncertain significance (Nov 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YTHDF1	protein_coding	protein_coding	ENST00000370339	5	20806

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00580	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	263	347	0.758	0.0000210	3708
Missense in Polyphen		70	135.88	0.51516		1451
Synonymous	-1.09	164	147	1.11	0.0000105	1086
Loss of Function	3.91	1	19.7	0.0507	8.47e-7	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000366	0.0000352
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 mRNAs, and promotes mRNA translation efficiency (PubMed:24284625, PubMed:26046440, PubMed:26318451). 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:24284625). Acts as a regulator of mRNA translation efficiency: promotes ribosome loading to m6A- containing mRNAs and interacts with translation initiation factors eIF3 (EIF3A or EIF3B) to facilitate translation initiation (PubMed:26046440). {ECO:0000269|PubMed:24284625, ECO:0000269|PubMed:26046440, ECO:0000269|PubMed:26318451}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0971
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.99

Haploinsufficiency Scores

• pHI: 0.197
• hipred: Y
• hipred_score: 0.673
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.915

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ythdf1

Gene ontology

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