TMEM39A

transmembrane protein 39A

Basic information

Region (hg38): 3:119428948-119468830

Links

ENSG00000176142 ∙ NCBI:55254 ∙ ∙ HGNC:25600 ∙ Uniprot:Q9NV64 ∙ 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 TMEM39A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM39A 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in TMEM39A

This is a list of pathogenic ClinVar variants found in the TMEM39A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-119432154-C-T		not specified	Uncertain significance (Mar 05, 2024)
3-119432159-C-T		not specified	Uncertain significance (Dec 20, 2021)
3-119434866-T-C		not specified	Uncertain significance (Mar 23, 2022)
3-119436851-G-A		not specified	Uncertain significance (Jan 05, 2022)
3-119436885-A-T		not specified	Uncertain significance (Sep 28, 2022)
3-119436960-T-C		not specified	Uncertain significance (May 27, 2022)
3-119437868-G-A		not specified	Uncertain significance (Jun 05, 2024)
3-119437901-T-C		not specified	Uncertain significance (Oct 04, 2022)
3-119438015-C-T		not specified	Uncertain significance (Nov 10, 2022)
3-119438024-C-T		not specified	Uncertain significance (Mar 07, 2023)
3-119438029-T-C		not specified	Uncertain significance (Jul 11, 2022)
3-119438062-C-T		not specified	Uncertain significance (May 03, 2023)
3-119447039-T-C		not specified	Uncertain significance (Oct 05, 2021)
3-119447070-C-T		not specified	Uncertain significance (Aug 23, 2021)
3-119447076-T-C		not specified	Uncertain significance (Aug 17, 2022)
3-119458086-G-T		not specified	Uncertain significance (Dec 17, 2023)
3-119458095-G-A		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM39A	protein_coding	protein_coding	ENST00000319172	8	39331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.955	0.0453	125732	0	7	125739	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	198	270	0.735	0.0000141	3159
Missense in Polyphen		65	115.04	0.56503		1349
Synonymous	0.709	93	102	0.911	0.00000521	983
Loss of Function	3.86	3	22.9	0.131	0.00000119	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000620	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000538	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.327
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.591
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.575

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem39a

Gene ontology

• Cellular component: integral component of membrane