TMEM42

transmembrane protein 42, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 3:44861904-44865670

Links

ENSG00000169964 ∙ NCBI:131616 ∙ ∙ HGNC:28444 ∙ Uniprot:Q69YG0 ∙ 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 TMEM42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM42 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in TMEM42

This is a list of pathogenic ClinVar variants found in the TMEM42 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-44861937-C-T		not specified	Uncertain significance (May 03, 2023)
3-44861938-C-T		not specified	Uncertain significance (Jun 27, 2022)
3-44861940-G-T		not specified	Uncertain significance (Feb 12, 2024)
3-44861941-G-A		not specified	Uncertain significance (Aug 30, 2021)
3-44861950-G-T		not specified	Uncertain significance (Feb 12, 2024)
3-44862012-G-T		not specified	Uncertain significance (Mar 30, 2024)
3-44862030-C-T		not specified	Uncertain significance (Dec 15, 2023)
3-44862073-G-A		not specified	Uncertain significance (Dec 21, 2023)
3-44862100-T-C		not specified	Uncertain significance (Dec 11, 2023)
3-44862108-G-C		not specified	Uncertain significance (Dec 20, 2023)
3-44864243-C-T		not specified	Uncertain significance (Jun 09, 2022)
3-44864256-G-A		not specified	Uncertain significance (Oct 04, 2022)
3-44864281-A-G		not specified	Uncertain significance (Apr 12, 2024)
3-44864321-C-T		not specified	Uncertain significance (Jun 09, 2022)
3-44865085-T-C		not specified	Uncertain significance (Sep 26, 2023)
3-44865109-C-A		not specified	Uncertain significance (Nov 10, 2022)
3-44865110-T-C		not specified	Uncertain significance (Jun 03, 2022)
3-44865122-C-G		not specified	Uncertain significance (Aug 17, 2022)
3-44865160-C-T		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM42	protein_coding	protein_coding	ENST00000302392	3	3802

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0808	0.767	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.141	67	70.3	0.953	0.00000362	1003
Missense in Polyphen		27	28.952	0.93257		365
Synonymous	0.0505	28	28.3	0.988	0.00000151	325
Loss of Function	1.04	2	4.35	0.460	1.85e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.240
• hipred: N
• hipred_score: 0.248
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.727

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem42
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Cellular component: integral component of membrane