LHFPL2

LHFPL tetraspan subfamily member 2, the group of LHFPL tetraspan proteins

Basic information

Region (hg38): 5:78485214-78770021

Links

ENSG00000145685 ∙ NCBI:10184 ∙ OMIM:609718 ∙ HGNC:6588 ∙ Uniprot:Q6ZUX7 ∙ 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 LHFPL2 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHFPL2 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 LHFPL2

This is a list of pathogenic ClinVar variants found in the LHFPL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-78488996-G-C		not specified	Uncertain significance (Apr 10, 2023)
5-78489015-C-A		not specified	Uncertain significance (Dec 19, 2022)
5-78489098-C-A		not specified	Uncertain significance (May 01, 2023)
5-78509948-A-G		not specified	Uncertain significance (Nov 17, 2022)
5-78510009-G-A		not specified	Uncertain significance (Apr 04, 2023)
5-78510057-A-C		not specified	Uncertain significance (Feb 28, 2024)
5-78510093-G-A		not specified	Uncertain significance (Mar 24, 2023)
5-78510108-C-G		not specified	Uncertain significance (Oct 10, 2023)
5-78510120-C-G		not specified	Uncertain significance (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHFPL2	protein_coding	protein_coding	ENST00000380345	2	284807

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0562	0.873	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	104	139	0.749	0.00000770	1481
Missense in Polyphen		32	54.169	0.59074		646
Synonymous	0.184	56	57.8	0.969	0.00000373	462
Loss of Function	1.51	3	7.45	0.403	3.19e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000205	0.000198
East Asian	0.0000556	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.0000556	0.0000544
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in female and male fertility. Involved in distal reproductive tract development. {ECO:0000250|UniProtKB:Q8BGA2}.
• Pathway: TYROBP Causal Network;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.559
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.411
• hipred: N
• hipred_score: 0.459
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.240

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lhfpl2
• Phenotype: reproductive system phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); digestive/alimentary phenotype; hearing/vestibular/ear phenotype; vision/eye phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: platelet degranulation;single fertilization;biological_process;development of primary female sexual characteristics;development of primary male sexual characteristics;positive regulation of fertilization
• Cellular component: cellular_component;plasma membrane;integral component of membrane;platelet alpha granule membrane
• Molecular function: molecular_function