TPCN1

two pore segment channel 1, the group of MicroRNA protein coding host genes|Two pore segment channels

Basic information

Region (hg38): 12:113221050-113298585

Links

ENSG00000186815 ∙ NCBI:53373 ∙ OMIM:609666 ∙ HGNC:18182 ∙ Uniprot:Q9ULQ1 ∙ 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 TPCN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPCN1 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	1	2
missense			35	3	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding			3			3
Total	0	0	38	4	2

Variants in TPCN1

This is a list of pathogenic ClinVar variants found in the TPCN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-113226803-C-T		not specified	Uncertain significance (Mar 07, 2024)
12-113226826-A-G		not specified	Uncertain significance (Aug 02, 2021)
12-113226835-G-A		not specified	Uncertain significance (Sep 22, 2022)
12-113226881-C-G		not specified	Uncertain significance (Apr 13, 2023)
12-113260373-G-A		not specified	Uncertain significance (Dec 26, 2023)
12-113260407-G-A		not specified	Uncertain significance (Feb 12, 2024)
12-113260499-A-G			Likely benign (Jun 19, 2018)
12-113266186-G-A		not specified	Uncertain significance (May 29, 2024)
12-113266226-A-G		not specified	Uncertain significance (Aug 30, 2021)
12-113266274-T-A		not specified	Uncertain significance (Feb 16, 2023)
12-113266274-T-C		not specified	Uncertain significance (May 27, 2022)
12-113266275-G-A		not specified	Uncertain significance (Dec 12, 2023)
12-113266286-C-T		not specified	Uncertain significance (Jun 11, 2021)
12-113266294-C-G		not specified	Uncertain significance (Sep 27, 2022)
12-113266321-G-A		not specified	Uncertain significance (Mar 15, 2024)
12-113266336-G-A		not specified	Uncertain significance (May 11, 2022)
12-113267844-T-A		not specified	Uncertain significance (May 04, 2022)
12-113267845-C-T			Benign (Jul 13, 2018)
12-113268752-T-A		not specified	Uncertain significance (Oct 26, 2022)
12-113268757-G-T		not specified	Uncertain significance (Feb 05, 2024)
12-113268865-G-A		not specified	Uncertain significance (Jan 23, 2023)
12-113268869-G-A		not specified	Uncertain significance (Aug 08, 2023)
12-113273259-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-113276971-A-G		not specified	Uncertain significance (Jul 13, 2022)
12-113277282-C-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPCN1	protein_coding	protein_coding	ENST00000550785	28	77536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00398	0.996	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	381	540	0.705	0.0000339	5808
Missense in Polyphen		132	231.77	0.56953		2466
Synonymous	-0.688	240	227	1.06	0.0000151	1728
Loss of Function	4.83	15	52.9	0.283	0.00000270	586

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000243
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000929	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nicotinic acid adenine dinucleotide phosphate (NAADP) receptor that may function as one of the major voltage-gated Ca(2+) channels (VDCC) across the lysosomal and endosomal membrane. {ECO:0000269|PubMed:19620632}.
• Pathway: Stimuli-sensing channels;Ion channel transport;Fibroblast growth factor-1;Transport of small molecules (Consensus)

Intolerance Scores

• loftool: 0.0929
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.2

Haploinsufficiency Scores

• pHI: 0.223
• hipred: Y
• hipred_score: 0.592
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.833

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpcn1
• Phenotype: hematopoietic system phenotype; normal phenotype; immune system phenotype

Gene ontology

• Biological process: positive regulation of autophagy;ion transmembrane transport;regulation of ion transmembrane transport;release of sequestered calcium ion into cytosol
• Cellular component: lysosome;lysosomal membrane;endosome;endosome membrane;integral component of membrane
• Molecular function: voltage-gated calcium channel activity;protein binding;identical protein binding;NAADP-sensitive calcium-release channel activity