LHFPL3

LHFPL tetraspan subfamily member 3, the group of LHFPL tetraspan proteins

Basic information

Region (hg38): 7:104328602-104908561

Previous symbols: [ "LHFPL4" ]

Links

ENSG00000187416 ∙ NCBI:375612 ∙ OMIM:609719 ∙ HGNC:6589 ∙ Uniprot:Q86UP9 ∙ 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 LHFPL3 gene.

• not provided (6 variants)
• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHFPL3 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			7	1		8
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	3	2

Variants in LHFPL3

This is a list of pathogenic ClinVar variants found in the LHFPL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-104328802-C-T		not specified	Uncertain significance (May 16, 2022)
7-104328820-C-A		not specified	Uncertain significance (Oct 14, 2021)
7-104328851-G-A			Benign (Dec 31, 2019)
7-104328936-G-T		not specified	Uncertain significance (Aug 16, 2022)
7-104328957-T-G		not specified	Uncertain significance (Oct 12, 2021)
7-104329001-G-C			Likely benign (Aug 18, 2018)
7-104329002-C-T			Uncertain significance (Apr 20, 2023)
7-104329077-C-T			Benign (Dec 27, 2018)
7-104329089-G-T			Likely benign (Dec 27, 2018)
7-104329104-T-G		not specified	Uncertain significance (Feb 07, 2023)
7-104736733-A-G			Likely benign (Dec 31, 2019)
7-104736821-T-G		not specified	Uncertain significance (Mar 01, 2024)
7-104736851-T-C		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHFPL3	protein_coding	protein_coding	ENST00000535008	5	579898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.932	0.0682	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	98	132	0.740	0.00000640	1530
Missense in Polyphen		31	50.992	0.60794		587
Synonymous	-0.415	57	53.2	1.07	0.00000262	469
Loss of Function	2.71	0	8.54	0.00	4.29e-7	100

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0814

Haploinsufficiency Scores

• pHI: 0.376
• hipred: N
• hipred_score: 0.427
• ghis: 0.576

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.328

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lhfpl3

Gene ontology

• Cellular component: integral component of membrane