TLCD5

TLC domain containing 5, the group of TLC domain containing

Basic information

Region (hg38): 11:120325296-120333686

Previous symbols: [ "TMEM136" ]

Links

ENSG00000181264 ∙ NCBI:219902 ∙ ∙ HGNC:28280 ∙ Uniprot:Q6ZRR5 ∙ 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 TLCD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLCD5 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in TLCD5

This is a list of pathogenic ClinVar variants found in the TLCD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-120327386-G-A		not specified	Uncertain significance (Jun 19, 2024)
11-120327434-A-G		not specified	Uncertain significance (Apr 04, 2023)
11-120327494-C-T		not specified	Uncertain significance (Apr 04, 2024)
11-120327500-A-G		not specified	Uncertain significance (May 09, 2024)
11-120327506-C-A		not specified	Uncertain significance (Jul 19, 2022)
11-120327535-T-C		not specified	Uncertain significance (Dec 21, 2022)
11-120327580-T-C		not specified	Uncertain significance (Dec 28, 2022)
11-120327602-T-C		not specified	Uncertain significance (Oct 21, 2021)
11-120329986-A-G		not specified	Uncertain significance (Jan 31, 2024)
11-120329989-C-T		not specified	Uncertain significance (Jul 20, 2021)
11-120330004-A-G		not specified	Uncertain significance (Feb 28, 2024)
11-120330054-G-A		not specified	Likely benign (Mar 02, 2023)
11-120330187-A-G		not specified	Uncertain significance (Nov 09, 2023)
11-120330205-G-A		not specified	Uncertain significance (Mar 13, 2023)
11-120330216-C-T		not specified	Uncertain significance (Apr 08, 2022)
11-120330232-A-G		not specified	Uncertain significance (Nov 03, 2022)
11-120330271-T-A		not specified	Uncertain significance (Aug 09, 2021)
11-120330306-G-A		not specified	Uncertain significance (Mar 29, 2023)
11-120330320-C-A		not specified	Uncertain significance (Mar 07, 2024)
11-120330337-C-T		not specified	Uncertain significance (Aug 29, 2023)
11-120330414-C-T		not specified	Uncertain significance (Feb 16, 2023)
11-120330415-G-A		not specified	Uncertain significance (Apr 08, 2024)
11-120330478-G-A		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLCD5	protein_coding	protein_coding	ENST00000314475	2	8554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00502	0.896	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.357	141	153	0.919	0.00000822	1762
Missense in Polyphen		49	47.255	1.0369		543
Synonymous	1.33	45	57.8	0.778	0.00000306	520
Loss of Function	1.41	5	9.74	0.513	5.02e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.460
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.280
• hipred: N
• hipred_score: 0.325
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.117

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem136
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Cellular component: integral component of membrane