TLCD1

TLC domain containing 1, the group of TLC domain containing

Basic information

Region (hg38): 17:28724348-28727935

Links

ENSG00000160606 ∙ NCBI:116238 ∙ ∙ HGNC:25177 ∙ Uniprot:Q96CP7 ∙ 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 TLCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLCD1 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			17			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	17	0	0

Variants in TLCD1

This is a list of pathogenic ClinVar variants found in the TLCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28724575-G-T		not specified	Uncertain significance (Oct 14, 2023)
17-28724578-G-T		not specified	Uncertain significance (Aug 16, 2022)
17-28724624-G-C		not specified	Uncertain significance (May 28, 2024)
17-28724797-T-A		not specified	Uncertain significance (Apr 12, 2024)
17-28724803-G-A		not specified	Uncertain significance (May 09, 2022)
17-28724809-T-C		not specified	Uncertain significance (Jan 10, 2023)
17-28724833-T-G		not specified	Uncertain significance (Nov 13, 2023)
17-28724848-C-T		not specified	Uncertain significance (Jun 28, 2023)
17-28724863-A-G		not specified	Uncertain significance (May 30, 2023)
17-28724866-A-C		not specified	Uncertain significance (Apr 07, 2023)
17-28725329-C-G		not specified	Uncertain significance (Dec 21, 2022)
17-28725339-G-C		not specified	Uncertain significance (May 06, 2024)
17-28725357-C-T		not specified	Uncertain significance (Oct 27, 2023)
17-28725368-G-A		not specified	Uncertain significance (Feb 10, 2022)
17-28725371-T-G		not specified	Uncertain significance (Sep 13, 2023)
17-28725911-G-C		not specified	Uncertain significance (Feb 10, 2022)
17-28725973-G-C		not specified	Uncertain significance (Dec 27, 2023)
17-28726019-A-G		not specified	Uncertain significance (May 23, 2023)
17-28726024-G-A		not specified	Uncertain significance (Mar 21, 2022)
17-28726058-C-T		not specified	Uncertain significance (Apr 10, 2023)
17-28726757-T-G		not specified	Uncertain significance (Aug 23, 2021)
17-28726774-C-A		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLCD1	protein_coding	protein_coding	ENST00000292090	4	3588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00443	0.881	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.232	136	144	0.946	0.00000800	1595
Missense in Polyphen		36	42.765	0.84181		507
Synonymous	-1.68	75	58.7	1.28	0.00000297	518
Loss of Function	1.34	5	9.44	0.529	4.51e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000140	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium channel facilitator that increases calcium flux by generating a larger window current and slowing inactivation of the L-type CACNA1C/CaV1.2 channel. Regulation of intracellular calcium by Calfacilitin is required for neural plate formation (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.169
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.251
• hipred: N
• hipred_score: 0.178
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tlcd1

Gene ontology

• Cellular component: plasma membrane;integral component of membrane