TLDC2

TBC/LysM-associated domain containing 2, the group of TLDc domain containing

Basic information

Region (hg38): 20:36876121-36894235

Previous symbols: [ "C20orf118" ]

Links

ENSG00000101342 ∙ NCBI:140711 ∙ ∙ HGNC:16112 ∙ Uniprot:A0PJX2 ∙ 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 TLDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLDC2 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			13	4	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding			23	25	6	54
Total	0	0	36	29	8

Variants in TLDC2

This is a list of pathogenic ClinVar variants found in the TLDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-36877933-A-T		not specified	Uncertain significance (Jul 19, 2022)
20-36877940-C-G		not specified	Uncertain significance (Jan 04, 2024)
20-36877996-C-G		not specified	Uncertain significance (Oct 05, 2023)
20-36878008-A-G		not specified	Uncertain significance (Nov 10, 2022)
20-36878013-A-G		not specified	Likely benign (Nov 18, 2022)
20-36878047-T-C		not specified	Uncertain significance (Oct 29, 2021)
20-36878049-C-T		not specified	Uncertain significance (Jan 22, 2024)
20-36879069-C-T		not specified	Uncertain significance (Oct 03, 2023)
20-36879096-G-T		not specified	Uncertain significance (Sep 20, 2023)
20-36879117-G-A		not specified	Uncertain significance (Oct 06, 2022)
20-36879123-A-T		not specified	Uncertain significance (May 31, 2023)
20-36879138-G-A		not specified	Likely benign (Oct 26, 2022)
20-36879145-G-C			Likely benign (Nov 01, 2022)
20-36879155-G-A			Benign (Jun 01, 2018)
20-36879188-G-A		not specified	Uncertain significance (Nov 03, 2023)
20-36879189-G-A		not specified	Uncertain significance (Jan 30, 2024)
20-36880665-C-G		not specified	Uncertain significance (Dec 09, 2023)
20-36889299-C-A			Likely benign (Nov 01, 2022)
20-36891924-G-C		Chilblain lupus 2 • Aicardi-Goutieres syndrome 5	Benign (Jan 12, 2018)
20-36892050-A-G		Aicardi-Goutieres syndrome 5 • Chilblain lupus 2	Uncertain significance (Jan 12, 2018)
20-36892061-C-T		Aicardi-Goutieres syndrome 5 • Chilblain lupus 2	Uncertain significance (Jan 12, 2018)
20-36892215-C-G		Aicardi-Goutieres syndrome 5 • Chilblain lupus 2	Uncertain significance (Jan 12, 2018)
20-36892221-T-G		Chilblain lupus 2 • Aicardi-Goutieres syndrome 5	Uncertain significance (Jan 13, 2018)
20-36892284-G-A		Chilblain lupus 2 • Aicardi-Goutieres syndrome 5	Uncertain significance (Feb 16, 2018)
20-36892303-G-A		Aicardi-Goutieres syndrome 5 • Chilblain lupus 2	Benign (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLDC2	protein_coding	protein_coding	ENST00000217320	6	18115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0165	0.962	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.297	142	132	1.07	0.00000803	1395
Missense in Polyphen		49	47.843	1.0242		568
Synonymous	0.214	52	54.0	0.963	0.00000340	425
Loss of Function	2.01	5	12.7	0.393	6.30e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.199
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tldc2