TANC1

tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1, the group of Ankyrin repeat domain containing|MicroRNA protein coding host genes|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 2:158968639-159232659

Links

ENSG00000115183 ∙ NCBI:85461 ∙ OMIM:611397 ∙ HGNC:29364 ∙ Uniprot:Q9C0D5 ∙ 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 TANC1 gene.

• Inborn genetic diseases (66 variants)
• not provided (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TANC1 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				7	2	9
missense			64	4	4	72
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	11	6

Variants in TANC1

This is a list of pathogenic ClinVar variants found in the TANC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-159065956-G-A		not specified	Likely benign (Nov 30, 2022)
2-159097729-T-C		not specified	Uncertain significance (Dec 07, 2021)
2-159097783-C-A			Benign (Dec 31, 2019)
2-159149163-C-T		not specified	Uncertain significance (Mar 02, 2023)
2-159149172-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-159149232-G-C		not specified	Uncertain significance (May 11, 2022)
2-159149251-T-C			Likely benign (Apr 01, 2022)
2-159150437-C-A		not specified	Uncertain significance (Jan 31, 2022)
2-159150480-G-A			Likely benign (Apr 01, 2022)
2-159150554-T-C		not specified	Uncertain significance (Jan 26, 2022)
2-159163390-C-T			Benign (Dec 31, 2019)
2-159163450-A-G		not specified	Uncertain significance (Dec 19, 2022)
2-159169256-G-A		not specified	Uncertain significance (Oct 25, 2023)
2-159169273-G-T		not specified	Uncertain significance (Oct 06, 2023)
2-159169290-C-T			Likely benign (Mar 01, 2023)
2-159169313-G-A		not specified	Uncertain significance (Jun 14, 2023)
2-159169316-C-T		not specified	Uncertain significance (Sep 28, 2022)
2-159169321-A-G		not specified	Uncertain significance (Dec 19, 2022)
2-159169364-A-T		not specified	Uncertain significance (May 24, 2023)
2-159170533-C-T		not specified	Uncertain significance (Apr 18, 2023)
2-159170638-T-A		not specified	Uncertain significance (Jan 24, 2024)
2-159170761-G-T		not specified	Uncertain significance (May 06, 2022)
2-159170764-T-A		not specified	Uncertain significance (Jul 25, 2023)
2-159170788-C-T		not specified	Uncertain significance (Oct 03, 2022)
2-159170793-T-G		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TANC1	protein_coding	protein_coding	ENST00000263635	25	264025

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000216	1.00	124729	0	73	124802	0.000293

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	934	1.05e+3	0.893	0.0000609	12120
Missense in Polyphen		353	446.53	0.79054		5080
Synonymous	0.243	435	441	0.985	0.0000295	3800
Loss of Function	5.71	24	78.7	0.305	0.00000422	935

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000931	0.000931
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.000233	0.000232
European (Non-Finnish)	0.000314	0.000309
Middle Eastern	0.000111	0.000111
South Asian	0.000131	0.000131
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a scaffold component in the postsynaptic density. {ECO:0000250}.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.526
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.27

Haploinsufficiency Scores

• pHI: 0.221
• hipred: Y
• hipred_score: 0.652
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0503

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tanc1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: myoblast fusion;visual learning;dendritic spine maintenance
• Cellular component: postsynaptic density;cell junction;dendrite;neuronal cell body;axon terminus;postsynaptic membrane
• Molecular function: protein binding