YLPM1

protein-coding

YLP motif containing 1, the group of Protein phosphatase 1 regulatory subunits

Gene summary

Enables RNA binding activity. Predicted to be involved in regulation of telomere maintenance. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in nuclear speck. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf170

MANE transcript

NM_019589.3

Inheritance

—

ClinVar variants

U:369B:14

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr14:74,763,316-74,859,435

External References & Databases

Ensembl (ENSG00000119596)

Transcript & Mutation Effects

hg38 • Region Span ~96.1 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 YLPM1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 348

not providedTotal: 11

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Myoepithelial tumorTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019589.3. 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			2 clinvar	4 clinvar	1 clinvar	7
missense			354 clinvar	8 clinvar	1 clinvar	363
nonsense			4 clinvar			4
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	369	12	2	383

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019589.3	RefSeq	NP_062535.2	20	MANE Select
ENST00000325680.12	Ensembl	ENSP00000324463.7	20	MANE Select
NM_001411052.1	RefSeq	NP_001397981.1	19	Standard
ENST00000547879.5	Ensembl	ENSP00000448367.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
biological_process

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
cytosol
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325680
Coding exons: 20
Length: 92176
Individuals with no LoFs: 124632
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 124660
p: 0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.768	1092	1.17e+3	0.937	0.0000619	13877
Missense (PolyPhen)		375	432.77	0.8665		5076
Synonymous	-0.646	414	398	1.04	0.0000193	4255
Loss of Function	7.72	18	102	0.176	0.00000647	1113

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00012	0.00011	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in the reduction of telomerase activity during differentiation of embryonic stem cells by binding to the core promoter of TERT and controlling its down-regulation. {ECO:0000250}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.119
RVIS EVS: -2.45
RVIS percentile EVS: 1.02

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.685

Gene Damage Prediction

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