TMEM163

transmembrane protein 163

Basic information

Region (hg38): 2:134455758-134719000

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

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.

• Inborn genetic diseases (13 variants)
• Leukodystrophy, hypomyelinating, 25 (1 variants)
• not provided (1 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.

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		1	14			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	14	0	0

Variants in TMEM163

This is a list of pathogenic ClinVar variants found in the TMEM163 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-134456750-A-G		not specified	Uncertain significance (Feb 28, 2024)
2-134456751-C-T		not specified	Uncertain significance (Dec 14, 2021)
2-134456756-G-A		not specified	Uncertain significance (Sep 01, 2021)
2-134458047-A-T		not specified	Uncertain significance (Apr 15, 2022)
2-134458057-G-C		not specified	Uncertain significance (Oct 28, 2023)
2-134458089-T-C		not specified	Uncertain significance (Aug 08, 2022)
2-134458150-C-T		not specified	Uncertain significance (Apr 05, 2023)
2-134466168-C-T		not specified	Uncertain significance (Aug 08, 2023)
2-134502978-C-T		not specified	Uncertain significance (Dec 28, 2023)
2-134502993-A-C			Uncertain significance (Jul 15, 2022)
2-134550582-T-C		not specified	Uncertain significance (Jan 06, 2023)
2-134550591-T-C		Leukodystrophy, hypomyelinating, 25	Pathogenic (Feb 14, 2023)
2-134550594-A-T		Leukodystrophy, hypomyelinating, 25	Uncertain significance (Mar 29, 2024)
2-134550616-G-A		Leukodystrophy, hypomyelinating, 25	Pathogenic (Feb 14, 2023)
2-134713295-A-C		Leukodystrophy, hypomyelinating, 25	Pathogenic (Feb 14, 2023)
2-134713295-A-G		Leukodystrophy, hypomyelinating, 25	Likely pathogenic (Nov 07, 2022)
2-134718745-A-C		not specified	Uncertain significance (Jul 11, 2023)
2-134718778-C-T		not specified	Uncertain significance (Sep 13, 2022)
2-134718783-C-G		not specified	Uncertain significance (Mar 22, 2023)
2-134718796-T-A		not specified	Uncertain significance (Sep 01, 2021)
2-134718826-C-T		not specified	Uncertain significance (Apr 14, 2022)
2-134718836-C-G		not specified	Uncertain significance (Dec 08, 2023)
2-134718850-G-A		not specified	Uncertain significance (Dec 07, 2021)
2-134718896-C-T		not specified	Uncertain significance (Apr 28, 2022)

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
0.0397	0.933	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

Haploinsufficiency Scores

• pHI: 0.305
• hipred: Y
• hipred_score: 0.736
• ghis: 0.570

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

Mouse Genome Informatics

• Gene name: Tmem163
• Phenotype: embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; pigmentation phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype; vision/eye phenotype; homeostasis/metabolism phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; craniofacial phenotype; cellular phenotype

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