TECPR2

tectonin beta-propeller repeat containing 2

Basic information

Region (hg38): 14:102362941-102502477

Previous symbols: [ "KIAA0329" ]

Links

ENSG00000196663 ∙ NCBI:9895 ∙ OMIM:615000 ∙ HGNC:19957 ∙ Uniprot:O15040 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary spastic paraplegia 49 (Strong), mode of inheritance: AR
• hereditary spastic paraplegia 49 (Strong), mode of inheritance: AR
• hereditary spastic paraplegia 49 (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neuropathy, hereditary sensory and autonomic, type IX, with developmental delay	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic	23176824; 26542466; 27406698; 32209221

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TECPR2 gene.

• Hereditary_spastic_paraplegia_49 (1274 variants)
• not_provided (149 variants)
• Inborn_genetic_diseases (135 variants)
• Hereditary_spastic_paraplegia (65 variants)
• not_specified (37 variants)
• TECPR2-related_disorder (27 variants)
• Intellectual_disability (2 variants)
• Sensory_autonomic_neuropathy_with_intellectual_disability (1 variants)
• Inherited_spastic_paresis (1 variants)
• Microcephaly (1 variants)
• See_cases (1 variants)
• Intellectual_disability,_FRA12A_type (1 variants)
• Autism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TECPR2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014844.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			12	652	6	670
missense	1		346	23	5	375
nonsense	23	6				29
start loss						0
frameshift	39	26				65
splice donor/acceptor (+/-2bp)		17				17
Total	63	49	358	675	11

Highest pathogenic variant AF is 0.00007750419

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TECPR2	protein_coding	protein_coding	ENST00000359520	19	139519

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.580	0.420	125670	0	78	125748	0.000310

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	689	830	0.830	0.0000502	9189
Missense in Polyphen		139	220.61	0.63008		2431
Synonymous	0.0224	366	367	0.999	0.0000259	2821
Loss of Function	5.60	13	59.7	0.218	0.00000256	697

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000339	0.000333
Ashkenazi Jewish	0.00322	0.00318
East Asian	0.000553	0.000544
Finnish	0.0000933	0.0000924
European (Non-Finnish)	0.000207	0.000202
Middle Eastern	0.000553	0.000544
South Asian	0.0000653	0.0000653
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably plays a role as positive regulator of autophagy. {ECO:0000269|PubMed:23176824}.

Intolerance Scores

• loftool: 0.518
• rvis_EVS: -0.47
• rvis_percentile_EVS: 22.84

Haploinsufficiency Scores

• pHI: 0.238
• hipred: Y
• hipred_score: 0.563
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.658

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tecpr2

Gene ontology

• Biological process: autophagy
• Molecular function: protein binding