LLPH

LLP homolog, long-term synaptic facilitation factor

Basic information

Region (hg38): 12:66116555-66130750

Previous symbols: [ "C12orf31" ]

Links

ENSG00000139233 ∙ NCBI:84298 ∙ OMIM:616998 ∙ HGNC:28229 ∙ Uniprot:Q9BRT6 ∙ 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 LLPH gene.

Variants pathogenicity by type

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

Variants in LLPH

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

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

Position	Type	Phenotype	Significance	ClinVar
12-66123862-A-T		not specified	Uncertain significance (Mar 31, 2024)
12-66123944-A-G		not specified	Uncertain significance (Jul 06, 2022)
12-66123949-G-A		not specified	Uncertain significance (Jan 24, 2023)
12-66123998-C-T		not specified	Uncertain significance (Oct 10, 2023)
12-66128932-G-T		not specified	Uncertain significance (Nov 18, 2022)
12-66128943-G-A		not specified	Uncertain significance (Nov 21, 2022)
12-66128959-C-T		not specified	Uncertain significance (Nov 17, 2022)
12-66129066-C-T		not specified	Uncertain significance (Feb 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LLPH	protein_coding	protein_coding	ENST00000266604	2	7707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.349	0.600	125385	2	312	125699	0.00125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.262	75	68.9	1.09	0.00000342	867
Missense in Polyphen		23	23.971	0.95949		337
Synonymous	0.669	16	19.8	0.809	8.47e-7	212
Loss of Function	1.53	1	4.51	0.222	1.89e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00191	0.00190
Ashkenazi Jewish	0.000856	0.000794
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00228	0.00218
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000334	0.0000327
Other	0.000869	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In hippocampal neurons, regulates dendritic and spine growth and synaptic transmission. {ECO:0000250|UniProtKB:Q9D945}.

Intolerance Scores

• loftool: 0.594
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.223
• hipred: N
• hipred_score: 0.206
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Llph

Gene ontology

• Biological process: positive regulation of dendritic spine development;dendrite extension
• Cellular component: chromosome;nucleolus
• Molecular function: basal RNA polymerase II transcription machinery binding;RNA binding