LHFPL3

protein-coding

LHFPL tetraspan subfamily member 3, 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. A partial gene fragment named LHFPL4 corresponds to a portion of the first exon of this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

LHFPL4

MANE transcript

NM_199000.3

Inheritance

—

ClinVar variants

U:24B:5

Top phenotype

Familial cancer of breast

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr7:104,328,603-104,908,561

External References & Databases

Ensembl (ENSG00000187416)

Transcript & Mutation Effects

hg38 • Region Span ~580.0 kb

Loading mutation effect viewer...

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 LHFPL3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 21

not providedTotal: 7

Familial cancer of breastTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_199000.3. 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				2 clinvar	2 clinvar	4
missense			22 clinvar	1 clinvar		23
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	3	2	29

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_199000.3	RefSeq	NP_945351.1	3	MANE Select
ENST00000424859.7	Ensembl	ENSP00000393128.2	3	MANE Select
NM_001386065.1	RefSeq	NP_001372994.1	3	Standard
ENST00000401970.3	Ensembl	ENSP00000385374.3	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: ENST00000535008
Coding exons: 5
Length: 579898
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.06	98	132	0.740	0.00000640	1530
Missense (PolyPhen)		31	50.992	0.60794		587
Synonymous	-0.415	57	53.2	1.07	0.00000262	469
Loss of Function	2.71	0	8.54	0.00	4.29e-7	100

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0814

Essentials

Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.328

Gene Damage Prediction

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