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.

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.

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	2	5
missense			136	3	1	140
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	137	6	3

Variants in YLPM1

This is a list of pathogenic ClinVar variants found in the YLPM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-74763512-A-G		not specified	Uncertain significance (Nov 22, 2022)
14-74763541-C-T		not specified	Uncertain significance (Jan 08, 2024)
14-74763542-C-G		not specified	Uncertain significance (Jun 13, 2023)
14-74763545-T-C		not specified	Uncertain significance (Jan 19, 2022)
14-74763568-C-G		not specified	Uncertain significance (Mar 20, 2024)
14-74763599-C-G		not specified	Uncertain significance (Nov 17, 2022)
14-74763730-C-T		not specified	Uncertain significance (Nov 18, 2022)
14-74763754-C-T		not specified	Uncertain significance (Nov 17, 2023)
14-74763770-G-A		not specified	Uncertain significance (Jan 04, 2022)
14-74763868-A-C		not specified	Uncertain significance (Aug 30, 2021)
14-74763883-C-G		not specified	Uncertain significance (Feb 07, 2023)
14-74763888-C-G		not specified	Uncertain significance (Jan 05, 2022)
14-74763910-A-G		not specified	Uncertain significance (Sep 01, 2021)
14-74763928-C-G		not specified	Uncertain significance (May 11, 2022)
14-74763929-C-G		not specified	Uncertain significance (Apr 11, 2023)
14-74763951-T-A			Benign (Jul 13, 2018)
14-74763959-A-G		not specified	Uncertain significance (Nov 19, 2022)
14-74763963-G-A		not specified	Uncertain significance (Oct 25, 2022)
14-74763973-C-G		not specified	Uncertain significance (Jun 16, 2024)
14-74763982-A-C		not specified	Uncertain significance (May 26, 2023)
14-74763985-C-G		not specified	Uncertain significance (Jan 26, 2023)
14-74763986-C-T		not specified	Uncertain significance (Aug 02, 2022)
14-74763992-C-T		not specified	Uncertain significance (Apr 15, 2024)
14-74764006-T-G		not specified	Uncertain significance (Oct 04, 2022)
14-74764027-T-C		not specified	Uncertain significance (May 06, 2022)

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