THNSL2

threonine synthase like 2

Basic information

Region (hg38): 2:88170295-88186636

Links

ENSG00000144115 ∙ NCBI:55258 ∙ OMIM:611261 ∙ HGNC:25602 ∙ Uniprot:Q86YJ6 ∙ 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 THNSL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THNSL2 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						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in THNSL2

This is a list of pathogenic ClinVar variants found in the THNSL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-88173188-T-C		not specified	Uncertain significance (Mar 31, 2024)
2-88173229-G-A		not specified	Uncertain significance (Jun 17, 2024)
2-88173244-C-T		not specified	Uncertain significance (May 18, 2022)
2-88173252-G-T		not specified	Uncertain significance (Jun 07, 2024)
2-88173299-C-T		not specified	Uncertain significance (May 08, 2023)
2-88173329-C-A		not specified	Uncertain significance (Mar 29, 2022)
2-88174651-G-A		not specified	Uncertain significance (Jan 10, 2023)
2-88174654-C-A		not specified	Uncertain significance (Apr 09, 2024)
2-88174697-G-C		not specified	Uncertain significance (Mar 14, 2024)
2-88174776-A-G		not specified	Likely benign (Apr 17, 2024)
2-88175297-C-T		not specified	Uncertain significance (Apr 07, 2022)
2-88175368-A-G		not specified	Uncertain significance (Jan 25, 2023)
2-88175390-A-T		not specified	Uncertain significance (Jun 05, 2024)
2-88178836-G-A		not specified	Uncertain significance (Mar 14, 2023)
2-88178950-G-A		not specified	Uncertain significance (Dec 07, 2021)
2-88179010-G-T		not specified	Uncertain significance (Jun 11, 2024)
2-88182764-A-G		not specified	Uncertain significance (Mar 20, 2024)
2-88182788-G-A		not specified	Uncertain significance (Mar 06, 2023)
2-88182967-G-T		not specified	Uncertain significance (Jul 19, 2023)
2-88185416-T-C		not specified	Uncertain significance (Dec 01, 2022)
2-88185905-C-G		not specified	Uncertain significance (Dec 17, 2023)
2-88185905-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-88185941-C-T		not specified	Uncertain significance (Mar 06, 2023)
2-88185948-C-T		not specified	Uncertain significance (Nov 10, 2021)
2-88185990-T-A		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THNSL2	protein_coding	protein_coding	ENST00000324166	8	16312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000148	0.856	124917	13	818	125748	0.00331

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0881	273	277	0.985	0.0000158	3152
Missense in Polyphen		87	80.951	1.0747		951
Synonymous	-0.426	123	117	1.05	0.00000722	974
Loss of Function	1.49	12	19.0	0.632	8.92e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00362	0.00362
Ashkenazi Jewish	0.00248	0.00248
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000538	0.000536
Middle Eastern	0.000109	0.000109
South Asian	0.0213	0.0211
Other	0.00294	0.00277

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: Acts as a catabolic phospho-lyase on both gamma- and beta-phosphorylated substrates. Degrades O-phospho- threonine (PThr) to alpha-ketobutyrate, ammonia and phosphate (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.550
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.23

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.219
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.504

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thnsl2

Zebrafish Information Network

• Gene name: thnsl2
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: biological_process;serine family amino acid catabolic process;regulation of signaling receptor activity;dephosphorylation;2-oxobutyrate biosynthetic process
• Cellular component: cellular_component;extracellular space
• Molecular function: molecular_function;threonine synthase activity;cytokine activity;pyridoxal phosphate binding;serine binding