TLCD4-RWDD3

TLCD4-RWDD3 readthrough

Basic information

Region (hg38): 1:95117923-95247225

Previous symbols: [ "TMEM56-RWDD3" ]

Links

ENSG00000271092 ∙ NCBI:100527978 ∙ ∙ HGNC:49388 ∙ ∙ ∙ 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 TLCD4-RWDD3 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLCD4-RWDD3 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			9	1		10
Total	0	0	9	1	0

Variants in TLCD4-RWDD3

This is a list of pathogenic ClinVar variants found in the TLCD4-RWDD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-95191635-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-95191650-A-G		not specified	Uncertain significance (Jan 04, 2024)
1-95191680-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-95191684-A-T		not specified	Uncertain significance (Jan 31, 2022)
1-95230935-G-T		not specified	Uncertain significance (Sep 29, 2022)
1-95230982-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-95234256-T-G		not specified	Uncertain significance (May 30, 2023)
1-95244217-A-G		not specified	Uncertain significance (Sep 29, 2023)
1-95244263-T-G		not specified	Uncertain significance (Dec 15, 2023)
1-95244274-C-A		not specified	Uncertain significance (Sep 16, 2021)
1-95244297-C-T		not specified	Uncertain significance (Sep 13, 2023)
1-95244307-A-G		not specified	Uncertain significance (Dec 20, 2023)
1-95244331-C-G		not specified	Uncertain significance (Jul 06, 2021)
1-95244345-C-A		not specified	Uncertain significance (Feb 15, 2023)
1-95244516-A-G		not specified	Uncertain significance (Aug 21, 2023)
1-95244528-A-G		not specified	Likely benign (Jun 12, 2023)
1-95244576-G-A		not specified	Uncertain significance (Aug 13, 2021)
1-95244662-A-G		not specified	Uncertain significance (Mar 25, 2024)
1-95246544-G-C		not specified	Uncertain significance (Oct 06, 2021)
1-95246633-C-T		not specified	Uncertain significance (Jul 08, 2022)
1-95246763-G-A		not specified	Uncertain significance (Mar 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLCD4-RWDD3	protein_coding	protein_coding	ENST00000604534	7	129303

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00823	0.937	125737	0	8	125745	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	74	105	0.708	0.00000525	1312
Missense in Polyphen		7	23.784	0.29432		289
Synonymous	1.02	31	39.1	0.792	0.00000212	378
Loss of Function	1.66	5	10.9	0.457	5.46e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000706	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Gene Damage Prediction

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

Gene ontology

• Cellular component: integral component of membrane