TECPR1

tectonin beta-propeller repeat containing 1

Basic information

Region (hg38): 7:98214623-98252232

Links

ENSG00000205356 ∙ NCBI:25851 ∙ OMIM:614781 ∙ HGNC:22214 ∙ Uniprot:Q7Z6L1 ∙ 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 TECPR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TECPR1 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				4	3	7
missense			90	2	1	93
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	90	6	4

Variants in TECPR1

This is a list of pathogenic ClinVar variants found in the TECPR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-98217430-G-A			Likely benign (Jan 01, 2023)
7-98217437-G-C		not specified	Uncertain significance (Aug 22, 2023)
7-98217500-C-T		not specified	Uncertain significance (Apr 13, 2023)
7-98217723-G-A		not specified	Uncertain significance (Dec 11, 2023)
7-98217762-C-T		not specified	Uncertain significance (Dec 19, 2022)
7-98217981-G-A			Likely benign (Apr 01, 2023)
7-98218031-A-C		not specified	Uncertain significance (Mar 29, 2022)
7-98221697-C-T		not specified	Uncertain significance (Jan 05, 2022)
7-98221714-C-T		not specified	Uncertain significance (Sep 27, 2021)
7-98221723-G-A		not specified	Uncertain significance (Jul 12, 2023)
7-98222492-G-T		not specified	Uncertain significance (Oct 10, 2023)
7-98222503-C-T		not specified	Uncertain significance (Feb 06, 2024)
7-98222992-C-T		not specified	Uncertain significance (Mar 01, 2024)
7-98223005-C-T			Benign (Apr 16, 2018)
7-98223018-C-A		not specified	Uncertain significance (Dec 01, 2022)
7-98223018-C-T		not specified	Uncertain significance (Nov 22, 2023)
7-98223019-G-A		Moyamoya angiopathy	Likely pathogenic (-)
7-98223079-C-T		not specified	Uncertain significance (Sep 26, 2023)
7-98223121-C-T		not specified	Uncertain significance (Sep 26, 2023)
7-98224849-G-A		not specified	Uncertain significance (Apr 12, 2022)
7-98224856-T-A		not specified	Uncertain significance (Jul 20, 2022)
7-98224874-C-T		Tracheoesophageal fistula	Likely pathogenic (Jul 01, 2019)
7-98225031-T-C		not specified	Uncertain significance (Sep 29, 2023)
7-98225034-G-A		not specified	Uncertain significance (Oct 27, 2022)
7-98225067-G-T		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TECPR1	protein_coding	protein_coding	ENST00000447648	24	37628

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.71e-7	1.00	125203	0	59	125262	0.000236

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	586	727	0.806	0.0000478	7465
Missense in Polyphen		143	235.06	0.60835		2400
Synonymous	-0.134	330	327	1.01	0.0000256	2250
Loss of Function	4.86	24	66.9	0.359	0.00000322	686

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000150
Ashkenazi Jewish	0.00122	0.00109
East Asian	0.0000633	0.0000551
Finnish	0.00	0.00
European (Non-Finnish)	0.000306	0.000291
Middle Eastern	0.0000633	0.0000551
South Asian	0.000358	0.000327
Other	0.000183	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tethering factor involved in autophagy. Involved in autophagosome maturation by promoting the autophagosome fusion with lysosomes: acts by associating with both the ATG5-ATG12 conjugate and phosphatidylinositol-3-phosphate (PtdIns(3)P) present at the surface of autophagosomes. Also involved in selective autophagy against bacterial pathogens, by being required for phagophore/preautophagosomal structure biogenesis and maturation. {ECO:0000269|PubMed:21575909, ECO:0000269|PubMed:22342342}.

Intolerance Scores

• rvis_EVS: -2.25
• rvis_percentile_EVS: 1.3

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.492
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.720

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tecpr1
• Phenotype: cellular phenotype; immune system phenotype

Gene ontology

• Biological process: autophagy;autophagosome maturation
• Cellular component: autophagosome membrane;nucleoplasm;lysosomal membrane;integral component of membrane;cytoplasmic vesicle;intracellular membrane-bounded organelle
• Molecular function: protein binding;phosphatidylinositol-3-phosphate binding