LHFPL6

protein-coding

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

Gene summary

This gene is a member of the lipoma HMGIC fusion partner (LHFP) gene family, which is a subset of the superfamily of tetraspan transmembrane protein encoding genes. This gene is fused to a high-mobility group gene in a translocation-associated lipoma. Mutations in another LHFP-like gene result in deafness in humans and mice. Alternatively spliced transcript variants have been found; however, their full-length nature is not known. [provided by RefSeq, Jul 2008]

Previous symbols:

LHFP

MANE transcript

NM_005780.3

Inheritance

—

ClinVar variants

U:29B:2

Top phenotype

LHFPL6-related disorder

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr13:39,209,116-39,603,528

External References & Databases

Ensembl (ENSG00000183722)

Transcript & Mutation Effects

hg38 • Region Span ~394.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LHFPL6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 25

LHFPL6-related disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005780.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			26 clinvar	1 clinvar		27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	29	1	1	31

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005780.3	RefSeq	NP_005771.1	3	MANE Select
ENST00000379589.4	Ensembl	ENSP00000368908.3	3	MANE Select
ENST00000648377.1	Ensembl	ENSP00000496801.1	3	Standard
ENST00000855017.1	Ensembl	ENSP00000525076.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379589
Coding exons: 3
Length: 260637
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125742
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.655	97	117	0.830	0.00000645	1270
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.1
RVIS percentile EVS: 46.2

Essentials

Essential (gene trap): N