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.

• not_specified (48 variants)
• Fraser_syndrome_3 (1 variants)

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. These statistics are base on transcript: NM_000024792.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			44	5		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	45	5	0

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