TMEM130

transmembrane protein 130

Basic information

Region (hg38): 7:98846488-98870771

Links

ENSG00000166448 ∙ NCBI:222865 ∙ ∙ HGNC:25429 ∙ Uniprot:Q8N3G9 ∙ 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 TMEM130 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM130 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in TMEM130

This is a list of pathogenic ClinVar variants found in the TMEM130 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-98848061-C-T		not specified	Uncertain significance (Jun 13, 2024)
7-98848087-A-C		not specified	Uncertain significance (Jun 16, 2023)
7-98848181-A-T		not specified	Uncertain significance (Nov 30, 2022)
7-98848220-T-G		not specified	Uncertain significance (Jan 23, 2024)
7-98848681-C-G		not specified	Uncertain significance (Nov 21, 2022)
7-98851433-C-T		not specified	Uncertain significance (Jun 10, 2024)
7-98851475-C-T		not specified	Uncertain significance (Mar 27, 2023)
7-98851477-G-T		not specified	Uncertain significance (Dec 21, 2023)
7-98851522-G-C		not specified	Uncertain significance (Dec 15, 2023)
7-98851534-G-A		not specified	Uncertain significance (Oct 18, 2021)
7-98851547-C-T		not specified	Uncertain significance (Aug 30, 2022)
7-98851616-G-C		not specified	Uncertain significance (Feb 06, 2024)
7-98851618-G-A		not specified	Uncertain significance (Apr 15, 2024)
7-98856079-G-A		not specified	Uncertain significance (Dec 03, 2021)
7-98856108-T-G		not specified	Uncertain significance (Jul 25, 2023)
7-98856119-C-T		not specified	Uncertain significance (Nov 03, 2023)
7-98856143-A-G		not specified	Uncertain significance (Nov 16, 2021)
7-98860267-T-A		not specified	Uncertain significance (Mar 22, 2022)
7-98860293-G-T		not specified	Uncertain significance (Jun 28, 2022)
7-98863107-G-A		not specified	Uncertain significance (Oct 04, 2022)
7-98863119-C-T		not specified	Likely benign (Nov 08, 2022)
7-98863185-C-T		not specified	Uncertain significance (Oct 03, 2022)
7-98863197-C-T		not specified	Uncertain significance (Feb 07, 2023)
7-98863238-C-T		not specified	Uncertain significance (May 31, 2023)
7-98863274-C-T		not specified	Uncertain significance (Sep 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM130	protein_coding	protein_coding	ENST00000416379	8	24284

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.40e-8	0.372	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.452	242	263	0.922	0.0000157	2823
Missense in Polyphen		76	88.426	0.85948		991
Synonymous	-0.270	122	118	1.03	0.00000837	889
Loss of Function	0.789	14	17.6	0.797	8.12e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000269	0.000268
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000870	0.000870
Finnish	0.000198	0.000185
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000870	0.000870
South Asian	0.000296	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.874
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.55

Haploinsufficiency Scores

• pHI: 0.283
• hipred: N
• hipred_score: 0.180
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: 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: Tmem130

Gene ontology

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