TECPR1

protein-coding

tectonin beta-propeller repeat containing 1

Gene summary

This gene encodes a tethering factor involved in autophagy. The encoded protein is found at autolysosomes, and is involved in targeting protein aggregates, damaged mitochondria, and bacterial pathogens for autophagy [provided by RefSeq, Nov 2012]

MANE transcript

NM_015395.3

Inheritance

—

ClinVar variants

P:2U:228B:13

Top phenotype

Esophageal atresia/tracheoesophageal fistula

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr7:98,214,624-98,252,232

External References & Databases

Ensembl (ENSG00000205356)

Transcript & Mutation Effects

hg38 • Region Span ~37.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TECPR1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 207

not providedTotal: 9

Esophageal atresia/tracheoesophageal fistulaTotal: 1

Moyamoya angiopathyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015395.3. 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			8 clinvar	5 clinvar	3 clinvar	16
missense		2 clinvar	210 clinvar	4 clinvar	1 clinvar	217
nonsense			3 clinvar			3
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	2	228	9	4	243

Highest pathogenic variant AF is 0.000013650657

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015395.3	RefSeq	NP_056210.1	24	MANE Select
ENST00000447648.7	Ensembl	ENSP00000404923.2	24	MANE Select
ENST00000415086.5	Ensembl	ENSP00000412675.1	2	Standard
ENST00000420697.1	Ensembl	ENSP00000396076.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

autophagy
autophagosome maturation

Molecular Function

protein binding
phosphatidylinositol-3-phosphate binding

Cellular Component

autophagosome membrane
nucleoplasm
lysosomal membrane
integral component of membrane
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000447648
Coding exons: 24
Length: 37628
Individuals with no LoFs: 125203
Homozygous LoFs: 0
Heterozygous LoFs: 59
Defined: 125262
p: 0.000236

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.86	586	727	0.806	0.0000478	7465
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0.000088	0.000058	rare
Ashkenazi Jewish	0.0012	0.0011	notable
East Asian	0.000063	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00031	0.00029	rare
South Asian	0.00036	0.00033	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.720

Gene Damage Prediction

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