LHFPL7

LHFPL tetraspan subfamily member 7, the group of LHFPL tetraspan proteins

Basic information

Region (hg38): 22:24935098-24946695

Previous symbols: [ "TMEM211" ]

Links

ENSG00000206069 ∙ NCBI:255349 ∙ ∙ HGNC:33725 ∙ Uniprot:Q6ICI0 ∙ 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 LHFPL7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHFPL7 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in LHFPL7

This is a list of pathogenic ClinVar variants found in the LHFPL7 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-24935490-C-T		not specified	Likely benign (May 10, 2024)
22-24935532-T-C		not specified	Uncertain significance (Jan 30, 2024)
22-24938266-C-T		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHFPL7	protein_coding	protein_coding	ENST00000407886	2	11586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0261	0.582	125735	0	11	125746	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.519	60	72.4	0.828	0.00000357	832
Missense in Polyphen		14	17.731	0.78956		250
Synonymous	-0.731	34	29.0	1.17	0.00000147	276
Loss of Function	0.0450	2	2.07	0.966	8.89e-8	20

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.616
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.67

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.122

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem211

Gene ontology

• Cellular component: integral component of membrane