LHFPL6

LHFPL tetraspan subfamily member 6, the group of LHFPL tetraspan proteins

Basic information

Region (hg38): 13:39209116-39603528

Previous symbols: [ "LHFP" ]

Links

ENSG00000183722 ∙ NCBI:10186 ∙ OMIM:606710 ∙ HGNC:6586 ∙ Uniprot:Q9Y693 ∙ 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 LHFPL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHFPL6 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					1	1
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	10	1	1

Variants in LHFPL6

This is a list of pathogenic ClinVar variants found in the LHFPL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-39343949-T-A		not specified	Uncertain significance (Dec 14, 2023)
13-39343950-G-C		not specified	Uncertain significance (Oct 10, 2023)
13-39344004-C-A		not specified	Uncertain significance (Dec 30, 2023)
13-39378467-G-A		not specified	Uncertain significance (Sep 01, 2021)
13-39378481-T-C		not specified	Uncertain significance (Jul 14, 2021)
13-39378494-G-C		not specified	Uncertain significance (Feb 15, 2023)
13-39378530-C-T		LHFPL6-related disorder	Likely benign (Jul 24, 2019)
13-39600834-C-G		not specified	Uncertain significance (May 24, 2023)
13-39600910-C-T		not specified	Uncertain significance (Apr 23, 2024)
13-39600979-C-T		not specified	Likely benign (Feb 27, 2023)
13-39600992-C-A		not specified	Uncertain significance (Sep 22, 2021)
13-39601008-C-T		not specified	Uncertain significance (Apr 12, 2022)
13-39601023-A-G		not specified	Uncertain significance (Nov 09, 2023)
13-39601174-G-A		LHFPL6-related disorder	Benign (Nov 11, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHFPL6	protein_coding	protein_coding	ENST00000379589	3	260637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.671	0.325	125739	0	3	125742	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.655	97	117	0.830	0.00000645	1270
Missense in Polyphen		45	59.996	0.75005		656
Synonymous	-0.117	49	48.0	1.02	0.00000291	411
Loss of Function	2.27	1	7.90	0.127	3.35e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.392
• hipred: N
• hipred_score: 0.353
• ghis: 0.678

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Lhfp

Gene ontology

• Cellular component: integral component of membrane