TMEM106A

transmembrane protein 106A

Basic information

Region (hg38): 17:43211835-43220041

Links

ENSG00000184988 ∙ NCBI:113277 ∙ ∙ HGNC:28288 ∙ Uniprot:Q96A25 ∙ 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 TMEM106A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM106A 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					1	1
missense			9	2	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	2

Variants in TMEM106A

This is a list of pathogenic ClinVar variants found in the TMEM106A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-43213058-C-A		not specified	Uncertain significance (Dec 08, 2023)
17-43213142-C-G		not specified	Uncertain significance (Jun 16, 2023)
17-43213177-G-A			Benign (May 24, 2018)
17-43213849-C-T		not specified	Uncertain significance (Mar 25, 2024)
17-43213852-T-C		not specified	Uncertain significance (Mar 04, 2024)
17-43215843-G-A		not specified	Likely benign (Jan 17, 2024)
17-43215862-G-C		not specified	Uncertain significance (May 03, 2023)
17-43215897-T-A		not specified	Uncertain significance (Feb 05, 2024)
17-43216449-A-G		not specified	Uncertain significance (May 08, 2024)
17-43216474-A-C		not specified	Uncertain significance (Sep 22, 2023)
17-43216502-G-C			Benign (May 24, 2018)
17-43216701-T-C		not specified	Uncertain significance (Jun 27, 2023)
17-43216704-A-T		not specified	Uncertain significance (Dec 04, 2021)
17-43216724-C-T		not specified	Likely benign (Feb 27, 2024)
17-43216729-T-A		not specified	Uncertain significance (May 13, 2024)
17-43217304-G-T		not specified	Uncertain significance (May 30, 2024)
17-43217710-A-G		not specified	Uncertain significance (Sep 25, 2023)
17-43217736-T-C		not specified	Uncertain significance (Apr 04, 2024)
17-43217763-G-A		not specified	Likely benign (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM106A	protein_coding	protein_coding	ENST00000331615	7	8208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.84e-7	0.255	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.583	125	145	0.864	0.00000794	1700
Missense in Polyphen		45	48.38	0.93014		619
Synonymous	1.83	43	61.2	0.703	0.00000347	536
Loss of Function	0.328	11	12.2	0.899	6.21e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000217	0.000217
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: TYROBP Causal Network (Consensus)

Intolerance Scores

• loftool: 0.834
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem106a

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of membrane
• Molecular function: molecular_function