TMEM39B

transmembrane protein 39B, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:32072031-32102866

Links

ENSG00000121775 ∙ NCBI:55116 ∙ ∙ HGNC:25510 ∙ Uniprot:Q9GZU3 ∙ 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 TMEM39B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM39B 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in TMEM39B

This is a list of pathogenic ClinVar variants found in the TMEM39B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-32074957-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-32075014-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-32075035-A-T		not specified	Uncertain significance (Dec 02, 2022)
1-32075617-C-T		not specified	Uncertain significance (Apr 26, 2024)
1-32076805-A-G		not specified	Uncertain significance (Dec 20, 2023)
1-32076808-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-32076838-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-32077194-C-T		not specified	Uncertain significance (Aug 17, 2022)
1-32077234-C-T		not specified	Uncertain significance (Jul 27, 2022)
1-32077275-T-C		not specified	Uncertain significance (Mar 16, 2022)
1-32091751-A-G		not specified	Likely benign (Dec 06, 2022)
1-32091818-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-32091944-A-G		not specified	Uncertain significance (Oct 02, 2023)
1-32092006-G-A		not specified	Uncertain significance (Nov 06, 2023)
1-32094826-C-G		not specified	Uncertain significance (Nov 07, 2022)
1-32094854-T-G		not specified	Uncertain significance (Jul 14, 2021)
1-32094907-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-32094910-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-32094958-G-A		not specified	Uncertain significance (May 05, 2023)
1-32102596-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-32102635-G-C		not specified	Uncertain significance (Mar 15, 2023)
1-32102645-A-C		not specified	Uncertain significance (Dec 07, 2023)
1-32102669-C-T		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM39B	protein_coding	protein_coding	ENST00000336294	9	30836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00651	0.993	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	212	302	0.701	0.0000191	3205
Missense in Polyphen		52	115.51	0.45018		1234
Synonymous	-0.691	140	130	1.08	0.00000836	1014
Loss of Function	2.95	8	23.4	0.342	0.00000142	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000607	0.0000607
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000976	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.206
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.592
• hipred: Y
• hipred_score: 0.527
• ghis: 0.644

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem39b

Gene ontology

• Cellular component: integral component of membrane