YTHDF1

protein-coding

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

Gene summary

Enables N6-methyladenosine-containing RNA reader activity and ribosome binding activity. Involved in mRNA destabilization; positive regulation of translational initiation; and stress granule assembly. Located in P-body and cytoplasmic stress granule. Implicated in colorectal cancer. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C20orf21

MANE transcript

NM_017798.4

Inheritance

—

ClinVar variants

U:78B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr20:63,195,429-63,216,139

External References & Databases

Ensembl (ENSG00000149658)

Transcript & Mutation Effects

hg38 • Region Span ~20.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to YTHDF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 77

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017798.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	6 clinvar	9
missense			77 clinvar	2 clinvar	1 clinvar	80
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	5	7	90

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017798.4	RefSeq	NP_060268.2	5	MANE Select
ENST00000370339.8	Ensembl	ENSP00000359364.3	5	MANE Select
ENST00000370334.4	Ensembl	ENSP00000359359.4	4	Standard
ENST00000370334.5	Ensembl	ENSP00000359359.4	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of translation
positive regulation of translational initiation

Molecular Function

RNA binding
protein binding
ribosome binding
N6-methyladenosine-containing RNA binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370339
Coding exons: 5
Length: 20806
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.60	263	347	0.758	0.0000210	3708
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.915

Gene Damage Prediction

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