TMA16

translation machinery associated 16 homolog

Basic information

Region (hg38): 4:163494442-163520539

Previous symbols: [ "C4orf43" ]

Links

ENSG00000198498 ∙ NCBI:55319 ∙ ∙ HGNC:25638 ∙ Uniprot:Q96EY4 ∙ 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 TMA16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMA16 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			12	2	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	12	2	1

Variants in TMA16

This is a list of pathogenic ClinVar variants found in the TMA16 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-163507063-C-T		not specified	Uncertain significance (Jul 19, 2023)
4-163507112-C-T		not specified	Uncertain significance (Jun 26, 2024)
4-163512845-G-A		not specified	Uncertain significance (Dec 03, 2024)
4-163512852-C-A		not specified	Uncertain significance (Jun 07, 2024)
4-163515315-A-G		not specified	Uncertain significance (Jun 10, 2024)
4-163515356-C-T		not specified	Uncertain significance (Mar 12, 2025)
4-163515363-G-A			Benign (Jul 16, 2018)
4-163515428-C-T		not specified	Uncertain significance (Oct 18, 2021)
4-163515469-C-T			Benign (Jun 05, 2018)
4-163517435-G-C		not specified	Uncertain significance (Aug 28, 2024)
4-163517435-G-T		not specified	Uncertain significance (Jan 21, 2025)
4-163517458-G-A		not specified	Uncertain significance (Mar 07, 2024)
4-163519376-G-A		not specified	Uncertain significance (Oct 23, 2024)
4-163519389-G-A		not specified	Uncertain significance (Dec 09, 2023)
4-163519401-A-G		not specified	Likely benign (Jun 05, 2024)
4-163519428-A-G		not specified	Likely benign (Oct 19, 2024)
4-163519446-G-A		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMA16	protein_coding	protein_coding	ENST00000358572	7	26098

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000965	0.812	124768	0	20	124788	0.0000801

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.364	94	104	0.900	0.00000588	1335
Missense in Polyphen		20	25.475	0.7851		406
Synonymous	0.670	32	37.2	0.860	0.00000209	332
Loss of Function	1.21	8	12.7	0.632	6.84e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000322	0.000316
Ashkenazi Jewish	0.00	0.00
East Asian	0.000384	0.000334
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000658	0.0000618
Middle Eastern	0.000384	0.000334
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.42

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.239
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Mouse Genome Informatics

• Gene name: Tma16

Gene ontology

• Cellular component: nucleus;nucleolus
• Molecular function: protein binding