TECR

trans-2,3-enoyl-CoA reductase, the group of Steroid 5-alpha reductase family|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:14517084-14565980

Previous symbols: [ "SC2", "GPSN2" ]

Links

ENSG00000099797 ∙ NCBI:9524 ∙ OMIM:610057 ∙ HGNC:4551 ∙ Uniprot:Q9NZ01 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• intellectual disability, autosomal recessive 14 (Limited), mode of inheritance: AR
• intellectual disability, autosomal recessive 14 (Limited), mode of inheritance: AR
• intellectual disability (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 14	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; Neurologic	11590547; 18446860; 21212097

ClinVar

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

• not specified (12 variants)
• not provided (9 variants)
• Inborn genetic diseases (9 variants)
• Intellectual disability, autosomal recessive 14 (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TECR 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	6	1	8
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			5	1		6
non coding			1	1	1	3
Total	0	0	10	8	2

Variants in TECR

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

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

Position	Type	Phenotype	Significance	ClinVar
19-14518215-G-T		not specified	Uncertain significance (Dec 07, 2021)
19-14518231-C-G		not specified	Uncertain significance (Sep 29, 2022)
19-14518236-C-A		not specified	Uncertain significance (Sep 16, 2021)
19-14518262-G-A		not specified	Uncertain significance (Dec 28, 2023)
19-14518308-G-C			Benign (Dec 13, 2017)
19-14518319-G-T		not specified	Uncertain significance (Oct 22, 2021)
19-14518321-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-14518334-A-G		not specified	Uncertain significance (Nov 15, 2021)
19-14529713-TAAG-T		not specified	Uncertain significance (Dec 28, 2016)
19-14529721-G-A		not specified	Uncertain significance (Nov 18, 2016)
19-14562510-G-A		not specified • Intellectual disability, autosomal recessive 14	Likely benign (Mar 01, 2024)
19-14562539-C-T		not specified	Likely benign (Aug 22, 2016)
19-14563201-C-T		TECR-related disorder	Likely benign (Feb 26, 2020)
19-14563256-C-T		not specified	Uncertain significance (Aug 17, 2015)
19-14563675-G-A		not specified	Uncertain significance (Oct 25, 2023)
19-14563700-C-G		Intellectual disability, autosomal recessive 14	Uncertain significance (Feb 22, 2019)
19-14563813-G-A		not specified	Uncertain significance (Jun 29, 2015)
19-14563898-G-T		Intellectual disability, autosomal recessive 14 • not specified	Uncertain significance (Sep 16, 2021)
19-14563902-C-T		not specified	Uncertain significance (Nov 14, 2023)
19-14564167-G-A		not specified	Likely benign (Dec 11, 2023)
19-14564232-C-T		not specified	Uncertain significance (Jan 12, 2024)
19-14564260-C-A		not specified • TECR-related disorder	Benign (Jun 27, 2019)
19-14564287-G-A		not specified	Uncertain significance (Feb 20, 2024)
19-14564778-C-A			Likely benign (Jul 01, 2021)
19-14564793-C-T		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TECR	protein_coding	protein_coding	ENST00000215567	13	48896

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.108	0.891	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	116	184	0.631	0.0000131	1994
Missense in Polyphen		25	52.956	0.47209		675
Synonymous	-0.960	89	78.2	1.14	0.00000596	578
Loss of Function	3.21	6	22.4	0.268	0.00000117	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000914	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the last of the four reactions of the long- chain fatty acids elongation cycle. This endoplasmic reticulum- bound enzymatic process, allows the addition of 2 carbons to the chain of long- and very long-chain fatty acids/VLCFAs per cycle. This enzyme reduces the trans-2,3-enoyl-CoA fatty acid intermediate to an acyl-CoA that can be further elongated by entering a new cycle of elongation. Thereby, it participates in the production of VLCFAs of different chain lengths that are involved in multiple biological processes as precursors of membrane lipids and lipid mediators. {ECO:0000269|PubMed:12482854}.
• Disease: DISEASE: Mental retardation, autosomal recessive 14 (MRT14) [MIM:614020]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:21212097}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Biosynthesis of unsaturated fatty acids - Homo sapiens (human);Fatty acid elongation - Homo sapiens (human);Metabolism of lipids;Fatty acyl-CoA biosynthesis;Metabolism;Fatty acid metabolism;Synthesis of very long-chain fatty acyl-CoAs (Consensus)

Recessive Scores

• pRec: 0.735

Intolerance Scores

• loftool: 0.581
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.279
• hipred: Y
• hipred_score: 0.728
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tecr

Gene ontology

• Biological process: fatty acid elongation;long-chain fatty-acyl-CoA biosynthetic process;very long-chain fatty acid biosynthetic process;oxidation-reduction process
• Cellular component: nucleus;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of endoplasmic reticulum membrane
• Molecular function: protein binding;oxidoreductase activity;very-long-chain-acyl-CoA dehydrogenase activity;very-long-chain enoyl-CoA reductase activity