TRAPPC10

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

Basic information

Region (hg38): 21:44012309-44106552

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

ClinVar

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

not_specified (144 variants)
not_provided (9 variants)
Neurodevelopmental_disorder_with_microcephaly,_short_stature,_and_speech_delay (7 variants)
TRAPPC10-related_disorder (3 variants)
TRAPPopathy_microcephalic (1 variants)
NEURODEVELOPMENTAL_DISORDER_WITH_MICROCEPHALY,_SHORT_STATURE,_SPEECH_DELAY,_AND_BEHAVIORAL_ABNORMALITIES (1 variants)
Intellectual_disability (1 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. These statistics are base on transcript: NM_000003274.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	1 clinvar	4
missense		1 clinvar	140 clinvar	11 clinvar		152
nonsense		2 clinvar				2
start loss						0
frameshift	1 clinvar	1 clinvar				2
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	1	5	140	14	1

Highest pathogenic variant AF is 6.84235e-7

Loading clinvar variants...

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