TLCD3B

TLC domain containing 3B, the group of TLC domain containing

Basic information

Region (hg38): 16:30024427-30052978

Previous symbols: [ "FAM57B" ]

Links

ENSG00000149926 ∙ NCBI:83723 ∙ OMIM:615175 ∙ HGNC:25295 ∙ Uniprot:Q71RH2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cone-rod dystrophy (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cone-rod dystrophy 22	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	33077892

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TLCD3B gene.

• Cone-rod dystrophy 22 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLCD3B 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	1		11	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	11	1	0

Highest pathogenic variant AF is 0.00000657

Variants in TLCD3B

This is a list of pathogenic ClinVar variants found in the TLCD3B region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30025211-G-A		not specified	Uncertain significance (Apr 08, 2022)
16-30025221-G-A		not specified	Uncertain significance (Apr 06, 2024)
16-30025236-G-A		not specified	Uncertain significance (Mar 25, 2024)
16-30025460-T-C		not specified	Uncertain significance (Jun 27, 2023)
16-30026700-G-A		not specified	Uncertain significance (Dec 08, 2023)
16-30026709-G-A		not specified	Uncertain significance (Sep 12, 2023)
16-30026712-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-30026721-G-A		not specified	Likely benign (Mar 21, 2023)
16-30026725-C-T		not specified	Uncertain significance (Feb 28, 2024)
16-30026728-C-T		not specified	Uncertain significance (Jun 28, 2023)
16-30026818-GC-G		Cone-rod dystrophy 22	Pathogenic (Sep 16, 2021)
16-30029459-G-A		not specified	Uncertain significance (Jun 09, 2022)
16-30029469-T-G		not specified	Uncertain significance (Dec 15, 2023)
16-30029475-C-T		Cone-rod dystrophy 22	Pathogenic (May 04, 2022)
16-30030440-G-A		not specified	Uncertain significance (May 30, 2024)
16-30030455-G-A		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLCD3B	protein_coding	protein_coding	ENST00000380495	5	28552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.665	0.334	125723	0	7	125730	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	117	159	0.736	0.00000954	1744
Missense in Polyphen		37	63.393	0.58366		737
Synonymous	-0.0101	75	74.9	1.00	0.00000522	574
Loss of Function	2.71	2	12.2	0.164	6.07e-7	124

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)	0.0000532	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in ceramide synthesis. {ECO:0000250}.

Intolerance Scores

• loftool: 0.339
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.321
• hipred: N
• hipred_score: 0.442
• ghis: 0.708

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam57b

Zebrafish Information Network

• Gene name: fam57ba
• Affected structure: pigment cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of fat cell differentiation;ceramide biosynthetic process
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: sphingosine N-acyltransferase activity