TRAPPC10

trafficking protein particle complex subunit 10, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 21:44012308-44106552

Previous symbols: [ "TMEM1" ]

Links

ENSG00000160218 ∙ NCBI:7109 ∙ OMIM:602103 ∙ HGNC:11868 ∙ Uniprot:P48553 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with microcephaly, short stature, and speech delay (Limited), mode of inheritance: AR
• neurodevelopmental disorder with microcephaly, short stature, and speech delay (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC10 gene.

• Inborn genetic diseases (48 variants)
• not provided (5 variants)
• Neurodevelopmental disorder with microcephaly, short stature, and speech delay (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC10 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			47	5		52
nonsense		1				1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	2	47	5	2

Variants in TRAPPC10

This is a list of pathogenic ClinVar variants found in the TRAPPC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-44012503-T-C		not specified	Likely benign (Apr 07, 2023)
21-44012507-A-G		Neurodevelopmental disorder with microcephaly, short stature, and speech delay	Uncertain significance (-)
21-44012513-C-T		not specified	Uncertain significance (Jul 12, 2022)
21-44012522-C-T		not specified	Uncertain significance (Jul 20, 2021)
21-44032130-C-T		not specified	Uncertain significance (Sep 06, 2022)
21-44032144-C-T		not specified	Uncertain significance (May 25, 2022)
21-44032177-G-C		TRAPPC10-related disorder	Likely benign (Jun 20, 2023)
21-44052386-A-T		not specified	Uncertain significance (May 04, 2023)
21-44052388-G-A		not specified	Uncertain significance (Aug 02, 2022)
21-44052474-C-A		not specified	Uncertain significance (Mar 20, 2023)
21-44055756-G-A		not specified	Uncertain significance (Nov 28, 2023)
21-44055855-G-C		not specified	Uncertain significance (Feb 12, 2024)
21-44059134-A-G		not specified	Uncertain significance (Mar 02, 2023)
21-44059158-A-G		not specified	Uncertain significance (Sep 17, 2021)
21-44059208-G-T		not specified	Uncertain significance (Jan 18, 2023)
21-44059211-G-A		not specified	Uncertain significance (Jul 13, 2022)
21-44063667-G-A		not specified	Uncertain significance (Jul 13, 2022)
21-44063687-C-T		Neurodevelopmental disorder with microcephaly, short stature, and speech delay	Likely pathogenic (May 23, 2023)
21-44063744-G-A		not specified	Uncertain significance (Jul 14, 2023)
21-44074409-G-A		not specified	Uncertain significance (Jul 08, 2022)
21-44074445-G-A		not specified	Uncertain significance (May 05, 2023)
21-44075088-A-T		not specified	Uncertain significance (Apr 25, 2022)
21-44077711-A-T		not specified	Uncertain significance (Apr 05, 2023)
21-44077712-T-C		not specified	Uncertain significance (Feb 15, 2023)
21-44077783-A-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC10	protein_coding	protein_coding	ENST00000291574	23	94234

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000631	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	600	718	0.836	0.0000415	8277
Missense in Polyphen		111	208.47	0.53246		2400
Synonymous	-0.111	312	310	1.01	0.0000217	2446
Loss of Function	6.63	7	64.4	0.109	0.00000331	734

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.0000709	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.240
• rvis_EVS: -1.59
• rvis_percentile_EVS: 3.12

Haploinsufficiency Scores

• pHI: 0.317
• hipred: Y
• hipred_score: 0.580
• ghis: 0.647

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.518

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trappc10
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype; immune system phenotype; hematopoietic 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); vision/eye phenotype; limbs/digits/tail 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); digestive/alimentary phenotype; skeleton phenotype

Gene ontology

• Biological process: intra-Golgi vesicle-mediated transport;early endosome to Golgi transport;COPII vesicle coating;protein complex oligomerization
• Cellular component: Golgi membrane;cytosol;TRAPP complex;TRAPPII protein complex
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity