TMEM167A

transmembrane protein 167A

Basic information

Region (hg38): 5:83052845-83077863

Previous symbols: [ "TMEM167" ]

Links

ENSG00000174695 ∙ NCBI:153339 ∙ OMIM:620000 ∙ HGNC:28330 ∙ Uniprot:Q8TBQ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neonatal diabetes mellitus (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM167A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM167A 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

Variants in TMEM167A

This is a list of pathogenic ClinVar variants found in the TMEM167A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-83057121-C-T		not specified	Uncertain significance (Feb 17, 2024)
5-83065056-G-C		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM167A	protein_coding	protein_coding	ENST00000502346	4	25018

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000425	0.429	125713	0	5	125718	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.411	32	39.2	0.815	0.00000192	463
Missense in Polyphen		3	5.7921	0.51794		84
Synonymous	0.140	12	12.6	0.950	5.40e-7	131
Loss of Function	0.0428	5	5.10	0.980	2.82e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000895	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the early part of the secretory pathway. {ECO:0000269|PubMed:19942856}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.444
• ghis: 0.652

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000513

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem167
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein secretion;intracellular transport
• Cellular component: Golgi membrane;integral component of membrane