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

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.

• Lattice corneal dystrophy Type III (1 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	5	1	7
missense			23		5	28
nonsense						0
start loss						0
frameshift	1					1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			11	2	10	23
Total	1	0	36	7	16

Highest pathogenic variant AF is 0.0000197

Variants in TACSTD2

This is a list of pathogenic ClinVar variants found in the TACSTD2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-58575434-G-T		Lattice corneal dystrophy Type III	Likely benign (Jan 13, 2018)
1-58575470-T-TA		Corneal Dystrophy, Dominant/Recessive	Uncertain significance (Jun 14, 2016)
1-58575529-A-T		Lattice corneal dystrophy Type III	Uncertain significance (Jan 12, 2018)
1-58575540-A-G		Lattice corneal dystrophy Type III	Uncertain significance (Jan 13, 2018)
1-58575548-C-T		Lattice corneal dystrophy Type III	Benign (Jan 13, 2018)
1-58575620-C-A		Lattice corneal dystrophy Type III	Benign (Jan 13, 2018)
1-58575764-T-C		Lattice corneal dystrophy Type III	Benign (Jan 12, 2018)
1-58575789-A-G		Lattice corneal dystrophy Type III	Likely benign (Jan 13, 2018)
1-58575887-T-G		Lattice corneal dystrophy Type III	Uncertain significance (Jan 13, 2018)
1-58575904-T-G		Lattice corneal dystrophy Type III	Uncertain significance (Jan 12, 2018)
1-58575905-A-G		Lattice corneal dystrophy Type III	Benign (Jan 13, 2018)
1-58575949-G-C		Lattice corneal dystrophy Type III	Uncertain significance (Jan 13, 2018)
1-58575959-G-T		Lattice corneal dystrophy Type III	Benign (Jan 13, 2018)
1-58575983-T-C		Lattice corneal dystrophy Type III	Benign (Jan 12, 2018)
1-58576019-G-A		Lattice corneal dystrophy Type III	Benign (Jan 12, 2018)
1-58576087-G-A		Lattice corneal dystrophy Type III	Likely benign (Jan 12, 2018)
1-58576091-C-T		Lattice corneal dystrophy Type III	Uncertain significance (Jan 13, 2018)
1-58576126-T-G		Lattice corneal dystrophy Type III	Uncertain significance (Jan 13, 2018)
1-58576137-C-T		Lattice corneal dystrophy Type III	Benign (Jan 12, 2018)
1-58576179-G-A		Lattice corneal dystrophy Type III	Uncertain significance (Jan 13, 2018)
1-58576258-C-T		Lattice corneal dystrophy Type III • not specified	Conflicting classifications of pathogenicity (Sep 22, 2022)
1-58576268-T-C		Lattice corneal dystrophy Type III	Benign (Dec 12, 2023)
1-58576286-C-G		not specified	Uncertain significance (Dec 20, 2022)
1-58576298-C-T		not specified	Uncertain significance (Oct 27, 2022)
1-58576329-G-A		Lattice corneal dystrophy Type III	Benign (Dec 30, 2023)

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