TMEM132D

transmembrane protein 132D, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 12:129071725-129904025

Links

ENSG00000151952 ∙ NCBI:121256 ∙ OMIM:611257 ∙ HGNC:29411 ∙ Uniprot:Q14C87 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM132D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM132D gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.

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				2	3	5
missense			87	8	2	97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	87	10	5

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM132D	protein_coding	protein_coding	ENST00000422113	9	831942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000934	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.679	602	651	0.925	0.0000389	7232
Missense in Polyphen		118	168.08	0.70204		1930
Synonymous	-0.921	308	288	1.07	0.0000198	2201
Loss of Function	4.88	3	33.4	0.0897	0.00000172	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000314	0.000304
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May serve as a cell-surface marker for oligodendrocyte differentiation. {ECO:0000269|PubMed:12966072}.

Intolerance Scores

• loftool: 0.329
• rvis_EVS: -0.5
• rvis_percentile_EVS: 21.85

Haploinsufficiency Scores

• pHI: 0.287
• hipred: Y
• hipred_score: 0.711
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.388

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem132d

Gene ontology

• Biological process: negative regulation of phosphatase activity
• Cellular component: integral component of membrane
• Molecular function: protein binding