PELP1

proline, glutamate and leucine rich protein 1, the group of Armadillo like helical domain containing|Large ribosomal subunit biogenesis complex

Basic information

Region (hg38): 17:4669774-4704337

Links

ENSG00000141456 ∙ NCBI:27043 ∙ OMIM:609455 ∙ HGNC:30134 ∙ Uniprot:Q8IZL8 ∙ 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 PELP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PELP1 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			2	2		4
missense			21	3		24
nonsense			2			2
start loss						0
frameshift						0
inframe indel				2		2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	7	0

Variants in PELP1

This is a list of pathogenic ClinVar variants found in the PELP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4671982-G-A			Likely benign (Sep 01, 2022)
17-4672137-C-T		not specified	Uncertain significance (Jul 12, 2022)
17-4672143-C-T		not specified	Uncertain significance (Jan 17, 2024)
17-4672288-CTCT-C			Likely benign (Jan 01, 2023)
17-4672329-C-T		not specified	Uncertain significance (Feb 06, 2023)
17-4672544-G-A		not specified	Uncertain significance (Sep 12, 2023)
17-4672630-G-A			Likely benign (Sep 01, 2022)
17-4672631-C-T		not specified	Uncertain significance (Apr 23, 2024)
17-4672745-G-A		not specified	Uncertain significance (Jul 12, 2023)
17-4672754-G-A		not specified	Uncertain significance (Apr 19, 2024)
17-4672877-G-C		not specified	Uncertain significance (Sep 06, 2022)
17-4672921-G-GGGCATGGGGCCTGCTGAA			Likely benign (Jan 01, 2023)
17-4672946-G-T		not specified	Uncertain significance (Jul 19, 2023)
17-4672949-C-T		not specified	Uncertain significance (Jan 21, 2025)
17-4673024-G-A		not specified	Uncertain significance (Apr 09, 2024)
17-4673037-G-A		not specified	Uncertain significance (Jun 14, 2023)
17-4673071-G-A		not specified	Likely benign (Dec 25, 2024)
17-4673288-G-A		not specified	Uncertain significance (Feb 15, 2023)
17-4673327-G-A		not specified	Likely benign (Nov 07, 2023)
17-4673336-G-A		not specified	Uncertain significance (Feb 15, 2023)
17-4673430-CA-C		Global developmental delay	Uncertain significance (Jan 01, 2020)
17-4674615-C-T		not specified	Uncertain significance (Apr 19, 2024)
17-4674823-C-T		not specified	Uncertain significance (Jul 22, 2024)
17-4675304-G-A		not specified	Uncertain significance (Feb 10, 2025)
17-4676045-A-C		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PELP1	protein_coding	protein_coding	ENST00000574876	17	32954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000158	124589	0	12	124601	0.0000482

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	545	623	0.874	0.0000346	7073
Missense in Polyphen		135	202.09	0.668		2260
Synonymous	-1.08	286	264	1.08	0.0000150	2486
Loss of Function	5.56	2	39.9	0.0501	0.00000186	515

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000540	0.000540
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Coactivator of estrogen receptor-mediated transcription and a corepressor of other nuclear hormone receptors and sequence- specific transcription factors. Plays a role in estrogen receptor (ER) genomic activity when present in the nuclear compartment by activating the ER target genes in a hormonal stimulation dependent manner. Can facilitate ER non-genomic signaling via SRC and PI3K interaction in the cytosol. Plays a role in E2-mediated cell cycle progression by interacting with RB1. May have important functional implications in ER/growth factor cross-talk. Interacts with several growth factor signaling components including EGFR and HRS. Involved in nuclear receptor signaling via its interaction with AR and NR3C1. May promote tumorigenesis via its interaction with and modulation of several oncogenes including SRC, PI3K, STAT3 and EGFR. Plays a role in cancer cell metastasis via its ability to modulate E2-mediated cytoskeleton changes and cell migration via its interaction with SRC and PI3K. Functions as the key stabilizing component of the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMC complex is recruited to ZNF148 by methylated CHTOP, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes. Component of the PELP1 complex involved in the nucleolar steps of 28S rRNA maturation and the subsequent nucleoplasmic transit of the pre-60S ribosomal subunit. Regulates pre-60S association of the critical remodeling factor MDN1 (PubMed:21326211). {ECO:0000269|PubMed:11481323, ECO:0000269|PubMed:12415108, ECO:0000269|PubMed:12682072, ECO:0000269|PubMed:14963108, ECO:0000269|PubMed:15374949, ECO:0000269|PubMed:15456770, ECO:0000269|PubMed:15579769, ECO:0000269|PubMed:15994929, ECO:0000269|PubMed:16140940, ECO:0000269|PubMed:16352611, ECO:0000269|PubMed:16574651, ECO:0000269|PubMed:21326211, ECO:0000269|PubMed:22872859}.
• Pathway: Signaling by PTK6;Signal Transduction;pelp1 modulation of estrogen receptor activity;PTK6 Expression;AndrogenReceptor;Coregulation of Androgen receptor activity;Signaling by Non-Receptor Tyrosine Kinases;Plasma membrane estrogen receptor signaling;Nongenotropic Androgen signaling (Consensus)

Recessive Scores

• pRec: 0.0868

Haploinsufficiency Scores

• pHI: 0.0912
• hipred: Y
• hipred_score: 0.806
• ghis: 0.511

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.872

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pelp1

Gene ontology

• Biological process: rRNA processing;positive regulation of transcription by RNA polymerase II;cellular response to estrogen stimulus
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;transcriptionally active chromatin;MLL1 complex
• Molecular function: chromatin binding;RNA binding;protein binding;transcription factor binding