TACSTD2

tumor associated calcium signal transducer 2

Basic information

Region (hg38): 1:58575433-58577252

Previous symbols: [ "M1S1" ]

Links

ENSG00000184292

∙ NCBI:4070 ∙ OMIM:137290 ∙ HGNC:11530 ∙ Uniprot:P09758 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

gelatinous drop-like corneal dystrophy (Strong), mode of inheritance: AR
gelatinous drop-like corneal dystrophy (Supportive), mode of inheritance: AR
gelatinous drop-like corneal dystrophy (Definitive), mode of inheritance: AR
gelatinous drop-like corneal dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Corneal dystrophy, gelatinous drop-like	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	10192395; 12614764; 19693293; 20806038; 21541270

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TACSTD2 gene.

not_specified (53 variants)
Gelatinous_droplike_corneal_dystrophy (23 variants)
not_provided (10 variants)
TACSTD2-related_disorder (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TACSTD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002353.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar		2 clinvar	6 clinvar		9
missense	2 clinvar	1 clinvar	51 clinvar	4 clinvar	1 clinvar	59
nonsense	4 clinvar					4
start loss	1					1
frameshift	3 clinvar					3
splice donor/acceptor (+/-2bp)						0
Total	11	1	53	10	1

Highest pathogenic variant AF is 0.0000061993283

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TACSTD2	protein_coding	protein_coding	ENST00000371225	1	2068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00466	0.698	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.562	187	210	0.891	0.0000135	2020
Missense in Polyphen		61	69.467	0.87811		705
Synonymous	1.99	77	103	0.751	0.00000714	708
Loss of Function	0.690	4	5.79	0.691	2.48e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May function as a growth factor receptor.;
Disease: DISEASE: Corneal dystrophy, gelatinous drop-like (GDLD) [MIM:204870]: A form of lattice corneal dystrophy, a class of inherited stromal amyloidoses characterized by pathognomonic branching lattice figures in the cornea. GDLD is an autosomal recessive disorder characterized by severe corneal amyloidosis leading to blindness. Clinical manifestations, which appear in the first decade of life, include blurred vision, photophobia, and foreign-body sensation. By the third decade, raised, yellowish- gray, gelatinous masses severely impair visual acuity. {ECO:0000269|PubMed:10192395}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.256

Intolerance Scores

loftool: 0.617
rvis_EVS: 1.08
rvis_percentile_EVS: 91.8

Haploinsufficiency Scores

pHI: 0.341
hipred: N
hipred_score: 0.272
ghis: 0.443

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.522

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tacstd2
Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; neoplasm;

Gene ontology

Biological process: cell surface receptor signaling pathway;visual perception;cell population proliferation;negative regulation of epithelial cell migration;regulation of epithelial cell proliferation;negative regulation of stress fiber assembly;ureteric bud morphogenesis;negative regulation of branching involved in ureteric bud morphogenesis;cell-cell adhesion;negative regulation of substrate adhesion-dependent cell spreading;negative regulation of ruffle assembly;negative regulation of cell motility;positive regulation of stem cell differentiation
Cellular component: extracellular space;nucleus;cytosol;integral component of plasma membrane;bicellular tight junction;basal plasma membrane;membrane;lateral plasma membrane;extracellular exosome
Molecular function: protein binding;signaling receptor activity;cadherin binding involved in cell-cell adhesion