THYN1

thymocyte nuclear protein 1

Basic information

Region (hg38): 11:134248279-134253370

Links

ENSG00000151500 ∙ NCBI:29087 ∙ OMIM:613739 ∙ HGNC:29560 ∙ Uniprot:Q9P016 ∙ 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 THYN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THYN1 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in THYN1

This is a list of pathogenic ClinVar variants found in the THYN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-134248811-T-C		not specified	Likely benign (Apr 11, 2023)
11-134248851-G-C		not specified	Uncertain significance (Jan 23, 2024)
11-134248878-T-C		not specified	Uncertain significance (Apr 04, 2023)
11-134248905-T-C		not specified	Uncertain significance (Nov 06, 2023)
11-134248940-C-A		not specified	Uncertain significance (Feb 13, 2024)
11-134248940-C-T		not specified	Uncertain significance (Aug 14, 2023)
11-134249202-G-A		not specified	Uncertain significance (Nov 15, 2021)
11-134249232-G-C		not specified	Uncertain significance (Jul 25, 2023)
11-134249877-A-G		not specified	Uncertain significance (Nov 15, 2021)
11-134249916-C-T		not specified	Uncertain significance (Oct 12, 2022)
11-134250285-C-T		not specified	Uncertain significance (Nov 10, 2022)
11-134250321-G-C		not specified	Uncertain significance (Feb 17, 2022)
11-134250336-A-G		not specified	Uncertain significance (Jan 18, 2023)
11-134251156-G-A		not specified	Uncertain significance (Nov 12, 2021)
11-134251207-A-G		not specified	Uncertain significance (May 09, 2023)
11-134251244-C-G		not specified	Uncertain significance (Mar 30, 2022)
11-134251257-A-G		not specified	Likely benign (Apr 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THYN1	protein_coding	protein_coding	ENST00000341541	7	5092

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.97e-16	0.000543	125628	1	119	125748	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.185	120	126	0.954	0.00000670	1484
Missense in Polyphen		38	42.754	0.8888		554
Synonymous	-1.10	50	41.1	1.22	0.00000184	407
Loss of Function	-1.75	20	13.1	1.52	5.53e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00190	0.00190
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000325	0.000299
Middle Eastern	0.000381	0.000381
South Asian	0.000295	0.000261
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically binds 5-hydroxymethylcytosine (5hmC), suggesting that it acts as a specific reader of 5hmC. {ECO:0000250}.

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.208
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.197
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.261

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thyn1

Gene ontology

• Cellular component: nucleus