TMEM59L

transmembrane protein 59 like

Basic information

Region (hg38): 19:18607430-18621039

Previous symbols: [ "C19orf4" ]

Links

ENSG00000105696 ∙ NCBI:25789 ∙ OMIM:617096 ∙ HGNC:13237 ∙ Uniprot:Q9UK28 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMEM59L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM59L 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in TMEM59L

This is a list of pathogenic ClinVar variants found in the TMEM59L region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18612986-C-T		not specified	Uncertain significance (Nov 08, 2021)
19-18613071-A-T		not specified	Uncertain significance (Sep 12, 2023)
19-18613914-G-C		not specified	Uncertain significance (Dec 14, 2023)
19-18613966-T-G		not specified	Uncertain significance (Jul 19, 2023)
19-18613990-A-G		not specified	Uncertain significance (Mar 04, 2024)
19-18614008-G-A		not specified	Uncertain significance (Sep 22, 2022)
19-18614131-C-T		not specified	Uncertain significance (Jul 11, 2023)
19-18614173-C-T		not specified	Uncertain significance (Jun 05, 2024)
19-18615990-G-C		not specified	Uncertain significance (Feb 22, 2023)
19-18616019-C-A		not specified	Uncertain significance (Jan 24, 2023)
19-18616076-C-T			Benign (Apr 04, 2018)
19-18617033-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-18618206-C-G		not specified	Uncertain significance (Jan 24, 2024)
19-18618386-T-G		not specified	Uncertain significance (Apr 20, 2023)
19-18618424-G-A		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM59L	protein_coding	protein_coding	ENST00000600490	8	13610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000600	0.978	125706	1	36	125743	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.901	144	178	0.810	0.0000100	2167
Missense in Polyphen		56	72.127	0.77641		822
Synonymous	-0.0780	82	81.1	1.01	0.00000504	709
Loss of Function	2.03	8	17.0	0.469	9.49e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000221	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000934	0.0000924
European (Non-Finnish)	0.000180	0.000176
Middle Eastern	0.000272	0.000272
South Asian	0.000229	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates the O-glycosylation and complex N- glycosylation steps occurring during the Golgi maturation of APP. Inhibits APP transport to the cell surface and further shedding. {ECO:0000269|PubMed:20427278}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.720
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.235
• hipred: N
• hipred_score: 0.257
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.166

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem59l

Zebrafish Information Network

• Gene name: tmem59l
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased branchiness

Gene ontology

• Cellular component: Golgi membrane;membrane;integral component of membrane