TMEM163

transmembrane protein 163

Basic information

Region (hg38): 2:134455759-134719000

Links

ENSG00000152128 ∙ NCBI:81615 ∙ OMIM:618978 ∙ HGNC:25380 ∙ Uniprot:Q8TC26 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• leukodystrophy, hypomyelinating, 25 (Limited), mode of inheritance: AD
• leukodystrophy, hypomyelinating, 25 (Strong), mode of inheritance: AD
• leukodystrophy, hypomyelinating, 25 (Moderate), mode of inheritance: AD
• leukodystrophy, hypomyelinating, 25 (Moderate), mode of inheritance: AD
• leukodystrophy (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leukodystrophy, hypomyelinating, 25	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	35455965; 35953447

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM163 gene.

• not_specified (42 variants)
• Leukodystrophy,_hypomyelinating,_25 (7 variants)
• not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM163 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030923.5. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	1		3
missense	3	1	46	1		51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4			4
Total	3	1	52	2	0

Highest pathogenic variant AF is 6.840722e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM163	protein_coding	protein_coding	ENST00000281924	8	263241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	85	145	0.587	0.00000885	1859
Missense in Polyphen		23	54.37	0.42303		635
Synonymous	-0.00432	64	64.0	1.00	0.00000470	612
Loss of Function	1.91	4	10.8	0.372	4.56e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May bind zinc and other divalent cations and recruit them to vesicular organelles. {ECO:0000250}.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.267
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Gene ontology

• Biological process: zinc ion import into synaptic vesicle
• Cellular component: cell junction;integral component of synaptic vesicle membrane;early endosome membrane
• Molecular function: zinc ion binding