TLCD3A

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

Basic information

Region (hg38): 17:732412-742968

Previous symbols: [ "FAM57A" ]

Links

ENSG00000167695 ∙ NCBI:79850 ∙ OMIM:611627 ∙ HGNC:29646 ∙ Uniprot:Q8TBR7 ∙ 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 TLCD3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLCD3A 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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in TLCD3A

This is a list of pathogenic ClinVar variants found in the TLCD3A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-732687-G-A		not specified	Uncertain significance (Aug 12, 2021)
17-732711-G-C		not specified	Uncertain significance (Feb 05, 2024)
17-732756-A-T		not specified	Uncertain significance (Nov 17, 2022)
17-733132-G-T		not specified	Uncertain significance (Jan 19, 2024)
17-733175-C-T		not specified	Uncertain significance (Feb 23, 2023)
17-737890-T-C		not specified	Uncertain significance (May 05, 2023)
17-737891-G-A		not specified	Uncertain significance (Jan 18, 2023)
17-737902-C-T		Fraser syndrome 3	Uncertain significance (-)
17-737927-G-C		not specified	Uncertain significance (Oct 12, 2021)
17-737945-G-C		not specified	Uncertain significance (Jun 21, 2023)
17-738021-C-T		not specified	Uncertain significance (Jun 16, 2023)
17-738033-G-C		not specified	Uncertain significance (Nov 15, 2021)
17-738039-G-T		not specified	Uncertain significance (Jan 02, 2024)
17-740551-C-T		not specified	Likely benign (Sep 16, 2021)
17-740562-A-T		not specified	Uncertain significance (Nov 09, 2021)
17-741319-C-T		not specified	Uncertain significance (Dec 20, 2022)
17-741347-C-T		not specified	Uncertain significance (Jan 29, 2024)
17-741409-C-G		not specified	Uncertain significance (Aug 23, 2021)
17-741424-A-G		not specified	Uncertain significance (Dec 11, 2023)
17-741461-G-A		not specified	Uncertain significance (Dec 06, 2021)
17-741466-G-A		not specified	Likely benign (Nov 10, 2022)
17-741529-G-C		not specified	Uncertain significance (May 30, 2023)
17-741532-C-T		not specified	Uncertain significance (Jun 27, 2022)
17-741533-G-A		not specified	Uncertain significance (Oct 13, 2023)
17-741547-C-T		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLCD3A	protein_coding	protein_coding	ENST00000308278	5	10555

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.256	0.738	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.220	146	139	1.05	0.00000859	1641
Missense in Polyphen		56	58.145	0.96311		683
Synonymous	-0.459	62	57.6	1.08	0.00000356	542
Loss of Function	2.40	3	11.9	0.251	7.47e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000358	0.000358
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000703	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0866

Intolerance Scores

• loftool: 0.172
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.256
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.661

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam57a

Gene ontology

• Biological process: biological_process
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding