TMEM63C

transmembrane protein 63C

Basic information

Region (hg38): 14:77116568-77259495

Previous symbols: [ "C14orf171" ]

Links

ENSG00000165548 ∙ NCBI:57156 ∙ OMIM:619953 ∙ HGNC:23787 ∙ Uniprot:Q9P1W3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spastic paraplegia 87, autosomal recessive (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 87, autosomal recessive	AR	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	35718349

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM63C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM63C 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			34		1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	1

Variants in TMEM63C

This is a list of pathogenic ClinVar variants found in the TMEM63C region.

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

Position	Type	Phenotype	Significance	ClinVar
14-77133724-A-G		not specified	Uncertain significance (Sep 20, 2023)
14-77133808-C-A		not specified	Uncertain significance (Jul 15, 2021)
14-77133820-C-T		not specified	Uncertain significance (Nov 09, 2022)
14-77139317-A-G		not specified	Uncertain significance (Mar 31, 2022)
14-77139395-C-T		not specified	Uncertain significance (Mar 16, 2024)
14-77139479-G-A		not specified	Uncertain significance (Jan 05, 2022)
14-77139495-C-T		not specified	Likely benign (May 13, 2024)
14-77139549-T-C		not specified	Uncertain significance (Oct 02, 2023)
14-77139589-G-T		not specified	Uncertain significance (Nov 19, 2022)
14-77139590-T-C		not specified	Uncertain significance (Dec 21, 2023)
14-77139612-G-C		not specified	Uncertain significance (Apr 15, 2024)
14-77139672-A-G		not specified	Uncertain significance (Dec 16, 2023)
14-77218820-G-C		not specified	Uncertain significance (Oct 16, 2023)
14-77218829-G-C		not specified	Uncertain significance (May 17, 2023)
14-77218898-G-A		not specified	Uncertain significance (May 04, 2022)
14-77218952-G-A		not specified	Uncertain significance (Feb 28, 2024)
14-77219549-C-T		not specified	Uncertain significance (Apr 17, 2024)
14-77219550-G-T		not specified	Uncertain significance (Aug 28, 2023)
14-77219576-A-G		not specified	Uncertain significance (Feb 12, 2024)
14-77220061-T-C		not specified	Uncertain significance (Dec 15, 2022)
14-77225454-A-G		not specified	Benign (May 04, 2022)
14-77231622-G-A		not specified	Uncertain significance (Aug 21, 2023)
14-77231626-G-A		not specified	Uncertain significance (May 16, 2023)
14-77231634-A-G		not specified	Uncertain significance (Jan 03, 2024)
14-77233473-G-A		not specified	Uncertain significance (Jun 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM63C	protein_coding	protein_coding	ENST00000298351	22	142928

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.243	0.757	125267	0	13	125280	0.0000519

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	360	489	0.737	0.0000293	5317
Missense in Polyphen		114	187.52	0.60794		2012
Synonymous	0.169	191	194	0.985	0.0000127	1518
Loss of Function	4.63	10	42.6	0.235	0.00000191	493

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000208
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000538	0.0000529
Middle Eastern	0.0000557	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an osmosensitive calcium-permeable cation channel. {ECO:0000269|PubMed:24503647}.

Intolerance Scores

• loftool: 0.269
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.71

Haploinsufficiency Scores

• pHI: 0.232
• hipred: Y
• hipred_score: 0.806
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.261

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem63c

Gene ontology

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