TMEM63B

transmembrane protein 63B

Basic information

Region (hg38): 6:44126914-44155519

Previous symbols: [ "C6orf110" ]

Links

ENSG00000137216 ∙ NCBI:55362 ∙ OMIM:619952 ∙ HGNC:17735 ∙ Uniprot:Q5T3F8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Strong), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM63B gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM63B 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					1	1
missense	1	1	31			33
nonsense						0
start loss						0
frameshift			1			1
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	1	34	0	1

Variants in TMEM63B

This is a list of pathogenic ClinVar variants found in the TMEM63B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-44134714-G-A		TMEM63B-associated disorder • Rare epilepsy	Pathogenic/Likely pathogenic (Apr 24, 2024)
6-44135083-A-G		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
6-44135332-C-T		Inborn genetic diseases	Uncertain significance (Dec 16, 2021)
6-44135347-G-T			Uncertain significance (Feb 01, 2023)
6-44136384-G-A		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
6-44138502-C-T		Inborn genetic diseases	Uncertain significance (Nov 10, 2022)
6-44139526-G-A		Inborn genetic diseases	Uncertain significance (Aug 01, 2022)
6-44141040-C-G			Uncertain significance (Dec 21, 2023)
6-44146858-C-T		Inborn genetic diseases	Uncertain significance (Jun 07, 2023)
6-44146881-C-T		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
6-44146917-G-A		Inborn genetic diseases	Uncertain significance (Jun 13, 2022)
6-44147387-G-A			Likely benign (Jan 19, 2024)
6-44147457-C-T		Inborn genetic diseases	Uncertain significance (Sep 30, 2021)
6-44148299-A-C		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
6-44148309-C-T		Inborn genetic diseases	Uncertain significance (Dec 01, 2023)
6-44148589-G-A		Inborn genetic diseases	Uncertain significance (Jul 14, 2023)
6-44148608-A-C		Inborn genetic diseases	Uncertain significance (Dec 21, 2022)
6-44148809-G-T			Uncertain significance (Dec 03, 2023)
6-44148841-A-G		Inborn genetic diseases	Uncertain significance (Jan 17, 2024)
6-44148887-CCAT-C			Uncertain significance (Oct 24, 2023)
6-44148909-C-G			Uncertain significance (Mar 01, 2022)
6-44148919-G-A			Pathogenic (Sep 07, 2023)
6-44149874-C-G			Likely pathogenic (-)
6-44149887-C-T			Uncertain significance (Jan 01, 2024)
6-44150581-G-A		Inborn genetic diseases	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM63B	protein_coding	protein_coding	ENST00000259746	23	28606

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000821	125735	0	8	125743	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.22	243	511	0.475	0.0000309	5448
Missense in Polyphen		56	193.94	0.28874		2065
Synonymous	-1.14	234	213	1.10	0.0000136	1635
Loss of Function	5.88	3	46.1	0.0651	0.00000231	525

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	0.0000463	0.0000462
European (Non-Finnish)	0.0000542	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an osmosensitive calcium-permeable cation channel. {ECO:0000250}.
• Pathway: Fibroblast growth factor-1 (Consensus)

Intolerance Scores

• loftool: 0.0706
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.78

Haploinsufficiency Scores

• pHI: 0.283
• hipred: Y
• hipred_score: 0.673
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.519

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem63b
• Phenotype: vision/eye 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: ion transmembrane transport
• Cellular component: plasma membrane;actin cytoskeleton;integral component of membrane
• Molecular function: calcium activated cation channel activity