TMEM87A

transmembrane protein 87A, the group of 7TM uncharacterized proteins

Basic information

Region (hg38): 15:42210446-42273534

Links

ENSG00000103978 ∙ NCBI:25963 ∙ ∙ HGNC:24522 ∙ Uniprot:Q8NBN3 ∙ 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 TMEM87A gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM87A 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in TMEM87A

This is a list of pathogenic ClinVar variants found in the TMEM87A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-42211714-C-T		not specified	Uncertain significance (Aug 13, 2021)
15-42211740-T-A		not specified	Uncertain significance (Dec 20, 2023)
15-42219606-T-C		not specified	Uncertain significance (Oct 27, 2023)
15-42220070-T-G		not specified	Uncertain significance (Aug 15, 2023)
15-42226872-C-T		not specified	Uncertain significance (Dec 09, 2023)
15-42233268-G-A		not specified	Uncertain significance (May 17, 2023)
15-42233277-A-G		not specified	Uncertain significance (Apr 25, 2023)
15-42233290-T-C		not specified	Uncertain significance (Oct 26, 2022)
15-42237443-T-C		not specified	Uncertain significance (Jan 16, 2024)
15-42237447-A-G		not specified	Uncertain significance (Dec 13, 2023)
15-42237467-G-A		not specified	Uncertain significance (Oct 06, 2021)
15-42237523-C-G		not specified	Uncertain significance (Feb 12, 2024)
15-42237530-C-A		not specified	Uncertain significance (Oct 16, 2023)
15-42244061-T-C		not specified	Uncertain significance (Mar 01, 2024)
15-42244164-T-C		not specified	Uncertain significance (Feb 28, 2024)
15-42261242-G-A		not specified	Uncertain significance (Nov 15, 2021)
15-42264196-T-A		not specified	Uncertain significance (Dec 28, 2023)
15-42272075-T-C		not specified	Uncertain significance (May 26, 2023)
15-42273298-A-G		not specified	Uncertain significance (Jul 25, 2023)
15-42273341-G-A		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM87A	protein_coding	protein_coding	ENST00000389834	20	63132

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0815	0.919	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	223	290	0.770	0.0000142	3609
Missense in Polyphen		72	115.86	0.62143		1396
Synonymous	-0.728	111	102	1.09	0.00000481	1031
Loss of Function	4.32	10	39.2	0.255	0.00000207	453

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000824	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in retrograde transport from endosomes to the trans-Golgi network (TGN). {ECO:0000269|PubMed:26157166}.
• Pathway: miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• loftool: 0.148
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.356
• hipred: N
• hipred_score: 0.414
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.237

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem87a

Gene ontology

• Biological process: retrograde transport, endosome to Golgi
• Cellular component: cytosol;integral component of membrane;Golgi cisterna membrane