TACSTD2

protein-coding

tumor associated calcium signal transducer 2

Gene summary

This intronless gene encodes a carcinoma-associated antigen. This antigen is a cell surface receptor that transduces calcium signals. Mutations of this gene have been associated with gelatinous drop-like corneal dystrophy.[provided by RefSeq, Dec 2009]

Previous symbols:

M1S1

MANE transcript

NM_002353.3

Inheritance

ClinVar variants

P:12U:63B:11

Top phenotype

Corneal dystrophy, gelatinous drop-like

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr1:58,575,433-58,577,252

External References & Databases

Ensembl (ENSG00000184292)

Transcript & Mutation Effects

hg38 • Region Span ~1.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

gelatinous drop-like corneal dystrophyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008777

Submitter: G2P

gelatinous drop-like corneal dystrophySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008777

Submitter: PanelApp Australia

gelatinous drop-like corneal dystrophySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008777

Submitter: Labcorp Genetics (formerly Invitae)

gelatinous drop-like corneal dystrophySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008777

Submitter: Orphanet

gelatinous drop-like corneal dystrophyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008777

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Corneal dystrophy, gelatinous drop-likeAR

Manifestation: Ophthalmologic

Intervention: General

Rationale: 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

Refs: 10192395; 12614764; 19693293; 20806038; 21541270

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TACSTD2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 58

Gelatinous droplike corneal dystrophyTotal: 21

not providedTotal: 16

TACSTD2-related disorderTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002353.3. 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			3 clinvar	6 clinvar		9
missense	2 clinvar	1 clinvar	59 clinvar	4 clinvar	1 clinvar	67
nonsense	4 clinvar	1 clinvar				5
start loss	1 clinvar		1 clinvar			2
frameshift	3 clinvar					3
splice donor/acceptor (+/-2bp)						0
Total	10	2	63	10	1	86

Highest pathogenic variant AF is 0.0000061993283

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002353.3	RefSeq	NP_002344.2	1	MANE Select
ENST00000371225.4	Ensembl	ENSP00000360269.2	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell surface receptor signaling pathway
visual perception
cell population proliferation
negative regulation of epithelial cell migration
regulation of epithelial cell proliferation

Molecular Function

protein binding
signaling receptor activity
cadherin binding involved in cell-cell adhesion

Cellular Component

extracellular space
nucleus
cytosol
integral component of plasma membrane
bicellular tight junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371225
Coding exons: 1
Length: 2068
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	0.562	187	210	0.891	0.0000135	2020
Missense (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

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

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.522

Gene Damage Prediction

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