LHFPL1

protein-coding

LHFPL tetraspan subfamily member 1, 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. Mutations in one LHFP-like gene result in deafness in humans and mice, and a second LHFP-like gene is fused to a high-mobility group gene in a translocation-associated lipoma. Alternatively spliced transcript variants have been found, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

MANE transcript

NM_178175.4

Inheritance

—

ClinVar variants

U:74B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chrX:112,630,648-112,680,054

External References & Databases

Ensembl (ENSG00000182508)

Transcript & Mutation Effects

hg38 • Region Span ~49.4 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 LHFPL1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 25

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178175.4. 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			7 clinvar			7
missense			52 clinvar	1 clinvar		53
nonsense			6 clinvar			6
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	74	1	0	75

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178175.4	RefSeq	NP_835469.1	3	MANE Select
ENST00000371968.8	Ensembl	ENSP00000361036.3	3	MANE Select
ENST00000864007.1	Ensembl	ENSP00000534066.1	3	Standard
ENST00000864007.2	Ensembl	ENSP00000534066.1	3	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: ENST00000371968
Coding exons: 3
Length: 49500
Individuals with no LoFs: 125733
Homozygous LoFs: 4
Heterozygous LoFs: 8
Defined: 125745
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.474	75	87.5	0.857	0.00000653	1421
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00015	0.00012	rare
Latino/Admixed American	0.000037	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000026	rare
South Asian	0.00016	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.377
RVIS EVS: 0.24
RVIS percentile EVS: 68.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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