TMEM40

transmembrane protein 40

Basic information

Region (hg38): 3:12733527-12769457

Links

ENSG00000088726 ∙ NCBI:55287 ∙ ∙ HGNC:25620 ∙ Uniprot:Q8WWA1 ∙ 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 TMEM40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM40 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			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	0

Variants in TMEM40

This is a list of pathogenic ClinVar variants found in the TMEM40 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-12734778-T-C		not specified	Uncertain significance (Mar 27, 2023)
3-12735582-G-A		not specified	Uncertain significance (Mar 07, 2024)
3-12735600-C-T		not specified	Uncertain significance (Jun 29, 2023)
3-12735612-G-A		not specified	Uncertain significance (Dec 18, 2023)
3-12736584-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-12736587-A-T		not specified	Uncertain significance (Nov 07, 2022)
3-12736616-A-C		not specified	Uncertain significance (Aug 16, 2021)
3-12736632-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-12736772-T-C		not specified	Uncertain significance (Sep 23, 2023)
3-12736803-C-A		not specified	Uncertain significance (Feb 23, 2023)
3-12737713-T-C		not specified	Uncertain significance (May 08, 2024)
3-12737721-T-G		not specified	Uncertain significance (Aug 15, 2023)
3-12737743-C-G		not specified	Uncertain significance (Apr 23, 2024)
3-12737752-C-G		not specified	Uncertain significance (May 07, 2024)
3-12742463-G-A		not specified	Uncertain significance (Feb 26, 2024)
3-12743909-C-T		not specified	Likely benign (Nov 10, 2022)
3-12743911-T-C		not specified	Uncertain significance (Sep 29, 2023)
3-12743914-C-T		not specified	Uncertain significance (Sep 07, 2022)
3-12743915-C-T		not specified	Likely benign (Jun 05, 2024)
3-12743923-T-C		not specified	Uncertain significance (May 03, 2023)
3-12743937-G-C		not specified	Uncertain significance (Feb 28, 2023)
3-12743944-C-G		not specified	Uncertain significance (Oct 26, 2022)
3-12743944-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-12743965-G-C		not specified	Uncertain significance (Mar 01, 2023)
3-12748730-C-T		not specified	Likely benign (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM40	protein_coding	protein_coding	ENST00000314124	11	35933

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.48e-8	0.482	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.704	153	130	1.17	0.00000716	1489
Missense in Polyphen		50	42.649	1.1724		489
Synonymous	0.0358	51	51.3	0.994	0.00000291	446
Loss of Function	0.953	14	18.4	0.760	9.32e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000399	0.000398
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0984

Intolerance Scores

• loftool: 0.297
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.170
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.626

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem40

Gene ontology

• Cellular component: integral component of membrane