TAC3
Basic information
Region (hg38): 12:57010000-57028883
Previous symbols: [ "NKNB" ]
Links
Phenotypes
GenCC
Source:
- hypogonadotropic hypogonadism 7 with or without anosmia (Strong), mode of inheritance: AR
- hypogonadotropic hypogonadism (Supportive), mode of inheritance: AD
- hypogonadotropic hypogonadism 10 with or without anosmia (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Hypogonadotropic hypogonadism | AR | Endocrine | In Hypogonadotropic hypogonadism, surveillance in adolescence related to sexual maturation is indicated, as is monitoring of bone mineral density in order to allow early detection and treatment of disease | Endocrine | 19079066 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAC3 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 | 2 | |||||
missense | 10 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 1 | 1 | ||||
non coding | 6 | |||||
Total | 1 | 2 | 8 | 4 | 5 |
Highest pathogenic variant AF is 0.000348
Variants in TAC3
This is a list of pathogenic ClinVar variants found in the TAC3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-57010271-G-A | Benign (Mar 03, 2015) | |||
12-57010288-A-G | not specified | Likely benign (Mar 08, 2016) | ||
12-57012393-G-A | not specified | Uncertain significance (Aug 15, 2024) | ||
12-57012420-G-A | not specified | Uncertain significance (Jul 02, 2024) | ||
12-57012423-C-T | Uncertain significance (Jul 11, 2022) | |||
12-57012424-G-A | Likely benign (Jun 06, 2018) | |||
12-57012450-A-G | not specified | Benign (Jan 22, 2024) | ||
12-57012660-T-C | Benign (Jun 19, 2018) | |||
12-57012845-A-G | Hypogonadotropic hypogonadism 10 without anosmia | Pathogenic (Mar 01, 2009) | ||
12-57012866-T-C | Delayed puberty • Infertility disorder | Conflicting classifications of pathogenicity (Oct 01, 2023) | ||
12-57013358-C-G | Likely pathogenic (Sep 09, 2022) | |||
12-57013359-G-A | Hypogonadotropic hypogonadism 10 with or without anosmia | Uncertain significance (Jan 17, 2024) | ||
12-57013359-G-T | Hypogonadotropic hypogonadism 7 with or without anosmia • Delayed puberty | Likely pathogenic (Nov 01, 2014) | ||
12-57013365-C-T | TAC3-related disorder | Uncertain significance (Jan 14, 2023) | ||
12-57013366-G-A | Likely benign (Oct 01, 2022) | |||
12-57013379-T-A | not specified | Uncertain significance (Dec 13, 2023) | ||
12-57013379-T-C | not specified | Uncertain significance (May 18, 2023) | ||
12-57013389-C-G | Pathogenic (Jul 21, 2022) | |||
12-57013569-G-A | Likely benign (Apr 24, 2018) | |||
12-57013626-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
12-57013646-A-G | not specified | Uncertain significance (Oct 09, 2024) | ||
12-57013652-T-C | Hypogonadotropic hypogonadism 10 with or without anosmia | Uncertain significance (Apr 08, 2024) | ||
12-57015455-G-A | Benign (Jun 19, 2018) | |||
12-57015484-A-G | Likely benign (Apr 16, 2019) | |||
12-57015597-C-A | Benign (Jun 19, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TAC3 | protein_coding | protein_coding | ENST00000458521 | 5 | 18884 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0117 | 0.857 | 125719 | 0 | 29 | 125748 | 0.000115 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.690 | 50 | 65.7 | 0.761 | 0.00000373 | 791 |
Missense in Polyphen | 15 | 17.046 | 0.87998 | 217 | ||
Synonymous | -0.178 | 28 | 26.8 | 1.04 | 0.00000172 | 228 |
Loss of Function | 1.23 | 4 | 7.70 | 0.520 | 4.32e-7 | 85 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00153 | 0.00153 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00000879 | 0.00000879 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Tachykinins are active peptides which excite neurons, evoke behavioral responses, are potent vasodilators and secretagogues, and contract (directly or indirectly) many smooth muscles (By similarity). Is a critical central regulator of gonadal function. {ECO:0000250, ECO:0000269|PubMed:19079066}.;
- Disease
- DISEASE: Hypogonadotropic hypogonadism 10 with or without anosmia (HH10) [MIM:614839]: A disorder characterized by absent or incomplete sexual maturation by the age of 18 years, in conjunction with low levels of circulating gonadotropins and testosterone and no other abnormalities of the hypothalamic- pituitary axis. In some cases, it is associated with non- reproductive phenotypes, such as anosmia, cleft palate, and sensorineural hearing loss. Anosmia or hyposmia is related to the absence or hypoplasia of the olfactory bulbs and tracts. Hypogonadism is due to deficiency in gonadotropin-releasing hormone and probably results from a failure of embryonic migration of gonadotropin-releasing hormone-synthesizing neurons. In the presence of anosmia, idiopathic hypogonadotropic hypogonadism is referred to as Kallmann syndrome, whereas in the presence of a normal sense of smell, it has been termed normosmic idiopathic hypogonadotropic hypogonadism (nIHH). {ECO:0000269|PubMed:19079066, ECO:0000269|PubMed:23643382}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Signaling by GPCR;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Tachykinin receptors bind tachykinins;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i;G alpha (q) signalling events;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.181
Intolerance Scores
- loftool
- 0.380
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.64
Haploinsufficiency Scores
- pHI
- 0.0597
- hipred
- N
- hipred_score
- 0.153
- ghis
- 0.469
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.150
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tac2
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; normal phenotype; digestive/alimentary phenotype;
Gene ontology
- Biological process
- G protein-coupled receptor signaling pathway;tachykinin receptor signaling pathway;neuropeptide signaling pathway;female pregnancy
- Cellular component
- extracellular region;extracellular space
- Molecular function
- signaling receptor binding