TMEM38A

transmembrane protein 38A

Basic information

Region (hg38): 19:16661139-16690023

Links

ENSG00000072954 ∙ NCBI:79041 ∙ OMIM:611235 ∙ HGNC:28462 ∙ Uniprot:Q9H6F2 ∙ 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 TMEM38A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM38A 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 TMEM38A

This is a list of pathogenic ClinVar variants found in the TMEM38A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-16661272-G-T		not specified	Uncertain significance (Jun 29, 2023)
19-16661311-G-C		not specified	Uncertain significance (Jul 14, 2021)
19-16661335-G-C		not specified	Uncertain significance (May 23, 2024)
19-16680001-C-T		not specified	Uncertain significance (Sep 22, 2022)
19-16680005-G-A		not specified	Uncertain significance (Oct 21, 2024)
19-16680034-A-G		not specified	Uncertain significance (Dec 04, 2024)
19-16680108-C-G		not specified	Uncertain significance (Feb 24, 2022)
19-16680470-G-A		not specified	Uncertain significance (Dec 28, 2023)
19-16680497-C-T		not specified	Uncertain significance (Dec 14, 2022)
19-16680519-A-G		not specified	Uncertain significance (Nov 09, 2024)
19-16682432-G-T		not specified	Uncertain significance (Dec 16, 2021)
19-16682439-T-C		not specified	Uncertain significance (Mar 21, 2024)
19-16682460-T-C		not specified	Uncertain significance (Dec 19, 2023)
19-16682491-G-C		not specified	Uncertain significance (Oct 25, 2022)
19-16686293-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-16688168-C-A		not specified	Uncertain significance (Aug 10, 2021)
19-16688175-C-A		not specified	Uncertain significance (Feb 28, 2023)
19-16688178-C-G		not specified	Uncertain significance (Jan 23, 2023)
19-16688204-T-C		not specified	Uncertain significance (Nov 17, 2022)
19-16688273-G-A		not specified	Uncertain significance (Dec 19, 2022)
19-16688285-G-A		not specified	Uncertain significance (Mar 25, 2024)
19-16688337-G-A		not specified	Uncertain significance (Nov 25, 2024)
19-16688364-C-T		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM38A	protein_coding	protein_coding	ENST00000187762	6	28903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000583	0.907	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.929	138	172	0.801	0.00000971	1939
Missense in Polyphen		61	74.782	0.8157		826
Synonymous	-0.763	88	79.4	1.11	0.00000519	596
Loss of Function	1.49	7	12.8	0.548	7.14e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Monovalent cation channel required for maintenance of rapid intracellular calcium release. May act as a potassium counter-ion channel that functions in synchronization with calcium release from intracellular stores. {ECO:0000250|UniProtKB:Q3TMP8}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.16

Haploinsufficiency Scores

• pHI: 0.209
• hipred: N
• hipred_score: 0.390
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.305

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem38a
• Phenotype: muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: potassium ion transmembrane transport
• Cellular component: integral component of membrane;nuclear membrane;sarcoplasmic reticulum membrane;extracellular exosome
• Molecular function: potassium channel activity