TMEM178A

transmembrane protein 178A

Basic information

Region (hg38): 2:39664982-39717963

Previous symbols: [ "TMEM178" ]

Links

ENSG00000152154 ∙ NCBI:130733 ∙ ∙ HGNC:28517 ∙ Uniprot:Q8NBL3 ∙ 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 TMEM178A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM178A 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in TMEM178A

This is a list of pathogenic ClinVar variants found in the TMEM178A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-39666095-G-C		not specified	Uncertain significance (Jun 10, 2024)
2-39666127-C-G		not specified	Uncertain significance (May 15, 2023)
2-39666147-G-T		not specified	Uncertain significance (Feb 21, 2024)
2-39666185-C-T		not specified	Uncertain significance (Apr 30, 2024)
2-39666230-G-A		not specified	Uncertain significance (Apr 22, 2022)
2-39666290-C-T		not specified	Uncertain significance (Jun 27, 2022)
2-39666294-T-C		not specified	Uncertain significance (Jul 26, 2022)
2-39704107-A-C		not specified	Uncertain significance (Dec 22, 2023)
2-39704132-G-A		not specified	Uncertain significance (Feb 27, 2023)
2-39704138-G-A		not specified	Uncertain significance (Jul 26, 2022)
2-39704143-A-G		not specified	Uncertain significance (Apr 19, 2024)
2-39704158-A-T		not specified	Uncertain significance (Feb 27, 2024)
2-39717196-T-C		not specified	Uncertain significance (Jun 18, 2024)
2-39717199-T-C		not specified	Uncertain significance (Dec 08, 2023)
2-39717205-G-A		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM178A	protein_coding	protein_coding	ENST00000281961	4	52982

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.669	0.330	125282	0	3	125285	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	93	156	0.596	0.00000869	1877
Missense in Polyphen		21	55.004	0.38179		609
Synonymous	-1.30	83	69.3	1.20	0.00000423	626
Loss of Function	2.72	2	12.3	0.163	7.92e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000893	0.00000886
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a negative regulator of osteoclast differentiation in basal and inflammatory conditions by regulating TNFSF11-induced Ca (2+) fluxes, thereby controlling the induction of NFATC1. {ECO:0000250|UniProtKB:Q9CZ16}.

Haploinsufficiency Scores

• pHI: 0.307
• hipred: Y
• hipred_score: 0.745
• ghis: 0.673

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem178
• Phenotype: cellular phenotype; hematopoietic system phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: negative regulation of osteoclast differentiation;regulation of cytosolic calcium ion concentration
• Cellular component: endoplasmic reticulum membrane;integral component of membrane