TMEM106C

transmembrane protein 106C

Basic information

Region (hg38): 12:47963569-47968878

Links

ENSG00000134291 ∙ NCBI:79022 ∙ ∙ HGNC:28775 ∙ Uniprot:Q9BVX2 ∙ 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 TMEM106C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM106C 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in TMEM106C

This is a list of pathogenic ClinVar variants found in the TMEM106C region.

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

Position	Type	Phenotype	Significance	ClinVar
12-47964286-A-C		not specified	Uncertain significance (Jun 10, 2022)
12-47964402-G-A		not specified	Uncertain significance (Nov 12, 2021)
12-47965332-C-T		not specified	Uncertain significance (Apr 07, 2022)
12-47966114-A-G		not specified	Uncertain significance (Dec 21, 2022)
12-47966123-C-T		not specified	Uncertain significance (Sep 30, 2022)
12-47966148-C-G		not specified	Uncertain significance (Mar 11, 2024)
12-47966167-A-G		not specified	Uncertain significance (Oct 26, 2022)
12-47966690-T-G		not specified	Uncertain significance (Jul 25, 2023)
12-47966717-C-T		not specified	Uncertain significance (Sep 01, 2021)
12-47967217-C-G		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM106C	protein_coding	protein_coding	ENST00000429772	7	5310

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.50e-8	0.220	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.440	128	143	0.896	0.00000737	1621
Missense in Polyphen		49	54.384	0.901		685
Synonymous	0.239	55	57.3	0.960	0.00000314	501
Loss of Function	0.423	13	14.8	0.881	9.00e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000507	0.000507
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000382	0.000381
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000361	0.000360
Middle Eastern	0.000382	0.000381
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0899

Intolerance Scores

• loftool: 0.982
• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• pHI: 0.0916
• hipred: N
• hipred_score: 0.153
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.346

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem106c

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: molecular_function;protein binding