LACRT

protein-coding

lacritin

Gene summary

The protein encoded by this gene is highly expressed in the lacrimal glands and localized primarily to secretory granules and secretory fluid. It augments lacrimal acinar cell secretion, promotes ductal cell proliferation, and stimulates signaling through tyrosine phosphorylation and release of calcium. [provided by RefSeq, Jul 2008]

MANE transcript

NM_033277.2

Inheritance

—

ClinVar variants

U:25B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr12:54,630,811-54,634,895

External References & Databases

Ensembl (ENSG00000135413)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 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 LACRT variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 26

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033277.2. 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						0
missense			24 clinvar	2 clinvar		26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	25	2	0	27

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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_033277.2	RefSeq	NP_150593.1	5	MANE Select
ENST00000257867.5	Ensembl	ENSP00000257867.4	5	MANE Select
ENST00000546721.5	Ensembl	ENSP00000448193.1	4	Standard
ENST00000547511.5	Ensembl	ENSP00000447536.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein acetylation
positive regulation of cell population proliferation
regulation of signaling receptor activity
epithelial structure maintenance
positive regulation of macroautophagy

Molecular Function

fibronectin binding
protein binding
collagen binding
growth factor activity
laminin-1 binding

Cellular Component

extracellular region
extracellular space
secretory granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000257867
Coding exons: 5
Length: 4085
Individuals with no LoFs: 125692
Homozygous LoFs: 1
Heterozygous LoFs: 42
Defined: 125735
p: 0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.367	82	73.2	1.12	0.00000357	870
Missense (PolyPhen)		7	6.8164	1.0269		57
Synonymous	0.399	28	30.8	0.909	0.00000181	288
Loss of Function	0.111	6	6.30	0.952	2.65e-7	81

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.00075	0.00072	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Modulates secretion by lacrimal acinar cells.;

Recessive Scores

pRec: 0.0800

Intolerance Scores

LoFtool: 0.591
RVIS EVS: -0.14
RVIS percentile EVS: 42.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.601

Gene Damage Prediction

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