YLPM1

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

Basic information

Region (hg38): 14:74763316-74859435

Previous symbols: [ "C14orf170" ]

Links

ENSG00000119596 ∙ NCBI:56252 ∙ OMIM:619766 ∙ HGNC:17798 ∙ Uniprot:P49750 ∙ 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 YLPM1 gene.

• not_specified (298 variants)
• not_provided (6 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
• Myoepithelial_tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YLPM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000019589.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	1	5
missense			292	7	1	300
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	293	11	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YLPM1	protein_coding	protein_coding	ENST00000325680	20	92176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000351	124632	0	28	124660	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.768	1092	1.17e+3	0.937	0.0000619	13877
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000319	0.000319
Ashkenazi Jewish	0.0000997	0.0000993
East Asian	0.000116	0.000111
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000118	0.000115
Middle Eastern	0.000116	0.000111
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.418
• ghis: 0.650

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.685

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ylpm1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;biological_process
• Cellular component: nucleus;nucleoplasm;cytosol;nuclear speck
• Molecular function: RNA binding;protein binding