TLX1NB

TLX1 neighbor, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 10:101089321-101141438

Links

ENSG00000236311 ∙ NCBI:100038246 ∙ OMIM:612734 ∙ HGNC:37183 ∙ Uniprot:P0CAT3 ∙ 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 TLX1NB gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLX1NB 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	0	1	0

Variants in TLX1NB

This is a list of pathogenic ClinVar variants found in the TLX1NB region.

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

Position	Type	Phenotype	Significance	ClinVar
10-101089612-CT-C			Likely benign (Dec 01, 2022)
10-101131563-C-T		not specified	Uncertain significance (Jun 18, 2021)
10-101131674-T-C		not specified	Uncertain significance (Feb 14, 2024)
10-101131680-C-A		not specified	Uncertain significance (Nov 30, 2022)
10-101131731-G-A		not specified	Uncertain significance (Sep 22, 2022)
10-101131734-G-T		not specified	Uncertain significance (Mar 12, 2024)
10-101131737-A-C		not specified	Uncertain significance (Jul 09, 2021)
10-101131749-G-A		not specified	Uncertain significance (May 10, 2024)
10-101131777-C-T		not specified	Uncertain significance (Apr 22, 2022)
10-101131795-C-G		not specified	Uncertain significance (Jan 04, 2022)
10-101131876-G-C		not specified	Uncertain significance (Feb 15, 2023)
10-101131878-C-T		not specified	Uncertain significance (Mar 29, 2022)
10-101131896-A-G		not specified	Likely benign (Dec 28, 2022)
10-101131905-G-A		not specified	Uncertain significance (Feb 21, 2024)
10-101131941-G-A		not specified	Uncertain significance (May 30, 2024)
10-101131975-C-T		not specified	Uncertain significance (Dec 28, 2022)
10-101131978-A-C		not specified	Uncertain significance (Dec 07, 2021)
10-101134217-C-T		not specified	Uncertain significance (Sep 28, 2021)
10-101136717-C-T		not specified	Uncertain significance (Oct 26, 2021)
10-101136821-T-C		not specified	Uncertain significance (May 05, 2023)
10-101136891-C-T		not specified	Uncertain significance (Feb 28, 2024)
10-101136906-G-T		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLX1NB	protein_coding	protein_coding	ENST00000445873	1	41806

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0832	60	58.2	1.03	0.00000306	750
Missense in Polyphen		10	12.861	0.77752		172
Synonymous	-0.534	26	22.8	1.14	0.00000112	264
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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