TMEM132D

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

Basic information

Region (hg38): 12:129071724-129904025

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.

• Inborn genetic diseases (57 variants)
• not provided (11 variants)

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.

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			54	6	2	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	54	8	5

Variants in TMEM132D

This is a list of pathogenic ClinVar variants found in the TMEM132D region.

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

Position	Type	Phenotype	Significance	ClinVar
12-129073888-T-C		not specified	Likely benign (Nov 21, 2022)
12-129073901-T-C		not specified	Uncertain significance (Oct 27, 2022)
12-129073917-T-C		TMEM132D-related disorder	Likely benign (Jul 23, 2019)
12-129073920-G-A			Likely benign (Apr 10, 2018)
12-129073928-C-T			Uncertain significance (Apr 16, 2019)
12-129073949-C-A		not specified	Uncertain significance (Oct 29, 2021)
12-129073958-T-C		not specified	Uncertain significance (Aug 10, 2023)
12-129073967-C-T		not specified	Uncertain significance (Jan 10, 2023)
12-129073979-C-T		not specified	Uncertain significance (May 09, 2023)
12-129073992-G-A			Benign (Apr 05, 2018)
12-129074004-G-A		TMEM132D-related disorder	Benign (Sep 10, 2019)
12-129074021-C-T		not specified	Likely benign (Apr 25, 2022)
12-129074060-T-C		not specified	Uncertain significance (Feb 06, 2023)
12-129074172-T-C		TMEM132D-related disorder	Likely benign (Jul 22, 2023)
12-129074216-G-C		not specified	Uncertain significance (Dec 19, 2023)
12-129074422-A-G		not specified	Uncertain significance (Aug 04, 2023)
12-129074500-A-T		not specified	Uncertain significance (Feb 17, 2022)
12-129074515-C-T		not specified	Uncertain significance (Dec 07, 2021)
12-129074518-G-T		TMEM132D-related disorder	Benign (Feb 20, 2019)
12-129074537-T-A		not specified	Uncertain significance (Feb 28, 2024)
12-129074541-C-A		TMEM132D-related disorder	Benign (Nov 25, 2019)
12-129074565-G-C		not specified	Uncertain significance (Apr 17, 2023)
12-129074630-G-A		not specified	Uncertain significance (Aug 02, 2022)
12-129074683-G-A			Benign (May 21, 2018)
12-129074686-G-A		not specified	Uncertain significance (Jun 17, 2022)

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