THNSL1

threonine synthase like 1

Basic information

Region (hg38): 10:25016611-25026664

Links

ENSG00000185875 ∙ NCBI:79896 ∙ OMIM:611260 ∙ HGNC:26160 ∙ Uniprot:Q8IYQ7 ∙ 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 THNSL1 gene.

• Inborn genetic diseases (29 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THNSL1 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		1
missense			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in THNSL1

This is a list of pathogenic ClinVar variants found in the THNSL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-25023297-C-T		not specified	Uncertain significance (Feb 21, 2024)
10-25023330-C-T		not specified	Uncertain significance (Sep 13, 2023)
10-25023368-A-G		not specified	Uncertain significance (Nov 23, 2021)
10-25023424-G-A			Likely benign (Apr 01, 2022)
10-25023608-A-C		not specified	Uncertain significance (May 08, 2023)
10-25023657-T-C		not specified	Uncertain significance (Sep 17, 2021)
10-25023714-G-A		not specified	Uncertain significance (Jul 28, 2021)
10-25023750-A-G		not specified	Uncertain significance (Apr 22, 2022)
10-25023767-A-G		not specified	Uncertain significance (May 06, 2022)
10-25023779-C-A		not specified	Uncertain significance (Jan 08, 2024)
10-25023857-G-A		not specified	Uncertain significance (Mar 01, 2023)
10-25023906-C-T		not specified	Uncertain significance (Jun 06, 2023)
10-25023989-A-G		not specified	Uncertain significance (Mar 22, 2023)
10-25024033-G-C		not specified	Uncertain significance (Mar 28, 2023)
10-25024055-G-A		not specified	Uncertain significance (Aug 24, 2023)
10-25024094-A-G		not specified	Uncertain significance (Jul 15, 2021)
10-25024235-T-C		not specified	Uncertain significance (Oct 26, 2022)
10-25024275-A-C		not specified	Uncertain significance (Sep 29, 2023)
10-25024358-T-G		not specified	Uncertain significance (Aug 13, 2021)
10-25024380-T-C		not specified	Uncertain significance (Oct 05, 2023)
10-25024397-C-T		not specified	Uncertain significance (Oct 12, 2021)
10-25024411-T-A		not specified	Uncertain significance (Sep 22, 2021)
10-25024413-A-G		not specified	Uncertain significance (Jan 24, 2024)
10-25024428-C-T		not specified	Uncertain significance (Feb 17, 2024)
10-25024623-C-T		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THNSL1	protein_coding	protein_coding	ENST00000524413	1	10007

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-17	0.00569	125251	1	495	125747	0.00197

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.465	413	387	1.07	0.0000185	4896
Missense in Polyphen		164	150.57	1.0892		1937
Synonymous	-0.485	148	141	1.05	0.00000713	1439
Loss of Function	0.0243	26	26.1	0.995	0.00000159	317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00447	0.00446
Ashkenazi Jewish	0.00208	0.00209
East Asian	0.00353	0.00354
Finnish	0.000186	0.000185
European (Non-Finnish)	0.00195	0.00194
Middle Eastern	0.00353	0.00354
South Asian	0.00134	0.00134
Other	0.00441	0.00441

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0977

Intolerance Scores

• loftool: 0.588
• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.74

Haploinsufficiency Scores

• pHI: 0.0671
• hipred: N
• hipred_score: 0.350
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.887

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thnsl1

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function