LHFPL1

LHFPL tetraspan subfamily member 1, the group of LHFPL tetraspan proteins

Basic information

Region (hg38): X:112630648-112680054

Links

ENSG00000182508 ∙ NCBI:340596 ∙ OMIM:300566 ∙ HGNC:6587 ∙ Uniprot:Q86WI0 ∙ 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 LHFPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHFPL1 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in LHFPL1

This is a list of pathogenic ClinVar variants found in the LHFPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-112631425-G-A		not specified	Uncertain significance (Dec 21, 2023)
X-112631437-G-T		not specified	Uncertain significance (Jul 13, 2021)
X-112631471-C-T		not specified	Uncertain significance (Oct 06, 2022)
X-112631550-G-A		not specified	Uncertain significance (Oct 06, 2021)
X-112631592-C-T		not specified	Likely benign (Apr 12, 2022)
X-112660642-T-C		not specified	Uncertain significance (Aug 12, 2021)
X-112671114-C-A		not specified	Uncertain significance (May 18, 2023)
X-112671126-C-T		not specified	Uncertain significance (Mar 18, 2024)
X-112671342-G-A		not specified	Uncertain significance (May 18, 2023)
X-112671360-G-A		not specified	Uncertain significance (May 16, 2022)
X-112671386-C-T		not specified	Uncertain significance (Jun 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHFPL1	protein_coding	protein_coding	ENST00000371968	3	49500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.135	0.787	125733	4	8	125745	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.474	75	87.5	0.857	0.00000653	1421
Missense in Polyphen		23	34.804	0.66084		559
Synonymous	0.967	24	30.8	0.778	0.00000219	445
Loss of Function	1.43	2	5.66	0.353	3.58e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000160
Ashkenazi Jewish	0.00	0.00
East Asian	0.000216	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000371	0.0000264
Middle Eastern	0.000216	0.000163
South Asian	0.000161	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.377
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.419
• hipred: N
• hipred_score: 0.248
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lhfpl1
• Phenotype: skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Cellular component: integral component of membrane