TLCD2

TLC domain containing 2, the group of TLC domain containing

Basic information

Region (hg38): 17:1702815-1710377

Links

ENSG00000185561 ∙ NCBI:727910 ∙ ∙ HGNC:33522 ∙ Uniprot:A6NGC4 ∙ 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 TLCD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLCD2 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			15
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	0	0

Variants in TLCD2

This is a list of pathogenic ClinVar variants found in the TLCD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-1707848-C-G		not specified	Uncertain significance (Mar 23, 2022)
17-1707855-C-T		not specified	Uncertain significance (Mar 02, 2023)
17-1707906-C-T		not specified	Uncertain significance (Jul 12, 2022)
17-1708102-G-A		not specified	Uncertain significance (Oct 03, 2022)
17-1708104-G-A		not specified	Uncertain significance (Jan 18, 2022)
17-1708138-C-T		not specified	Uncertain significance (Apr 22, 2022)
17-1708177-C-T		not specified	Uncertain significance (Nov 08, 2022)
17-1708201-C-T		not specified	Uncertain significance (Apr 12, 2022)
17-1709501-C-A		not specified	Uncertain significance (Apr 06, 2024)
17-1709535-C-G		not specified	Uncertain significance (Aug 17, 2022)
17-1709837-G-T		not specified	Uncertain significance (Dec 09, 2023)
17-1709861-C-A		not specified	Uncertain significance (May 07, 2024)
17-1710068-C-T		not specified	Uncertain significance (Jun 03, 2024)
17-1710091-A-G		not specified	Uncertain significance (Nov 08, 2022)
17-1710092-G-A		not specified	Uncertain significance (Jun 21, 2022)
17-1710145-G-C		not specified	Uncertain significance (Sep 14, 2023)
17-1710208-G-A		not specified	Uncertain significance (Dec 21, 2023)
17-1710212-C-T		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLCD2	protein_coding	protein_coding	ENST00000330676	4	2669

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000609	0.277	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.693	125	149	0.840	0.00000792	1647
Missense in Polyphen		30	38.98	0.76962		552
Synonymous	0.876	57	66.1	0.863	0.00000328	605
Loss of Function	0.0487	8	8.15	0.982	3.51e-7	82

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.172

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0868

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tlcd2

Gene ontology

• Cellular component: integral component of membrane