LACRT

lacritin

Basic information

Region (hg38): 12:54630811-54634895

Links

ENSG00000135413 ∙ NCBI:90070 ∙ OMIM:607360 ∙ HGNC:16430 ∙ Uniprot:Q9GZZ8 ∙ 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 LACRT gene.

• not_specified (23 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LACRT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033277.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			21	2		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LACRT	protein_coding	protein_coding	ENST00000257867	5	4085

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000119	0.398	125692	1	42	125735	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.367	82	73.2	1.12	0.00000357	870
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.000163	0.000163
South Asian	0.000752	0.000719
Other	0.000490	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0721
• hipred: N
• hipred_score: 0.146
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.601

Gene Damage Prediction

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

Gene ontology

• Biological process: protein acetylation;positive regulation of cell population proliferation;regulation of signaling receptor activity;epithelial structure maintenance;positive regulation of macroautophagy;calcium-mediated signaling;negative regulation of lipopolysaccharide-mediated signaling pathway;calcineurin-NFAT signaling cascade;protein localization to Golgi apparatus;defense response to bacterium;negative regulation of apoptotic process;positive regulation of epithelial cell proliferation;positive regulation of peptidyl-tyrosine phosphorylation;positive regulation of calcium-mediated signaling;positive regulation of secretion;positive regulation of release of sequestered calcium ion into cytosol;positive regulation of epithelial cell proliferation involved in wound healing;tear secretion;positive regulation of calcineurin-NFAT signaling cascade
• Cellular component: extracellular region;extracellular space;secretory granule
• Molecular function: fibronectin binding;protein binding;collagen binding;growth factor activity;laminin-1 binding;protein N-terminus binding