TRAPPC14

trafficking protein particle complex subunit 14, the group of MicroRNA protein coding host genes|Trafficking protein particle complex subunits

Basic information

Region (hg38): 7:100154420-100158723

Previous symbols: [ "C7orf43", "MAP11" ]

Links

ENSG00000146826 ∙ NCBI:55262 ∙ OMIM:618350 ∙ HGNC:25604 ∙ Uniprot:Q8WVR3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive primary microcephaly (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly 25, primary, 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	30715179

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC14 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				3	1	4
missense			3	2		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	3	5	2

Variants in TRAPPC14

This is a list of pathogenic ClinVar variants found in the TRAPPC14 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100155046-C-T		not specified	Uncertain significance (Jan 24, 2024)
7-100155084-T-G		Microcephaly 25, primary, autosomal recessive	Uncertain significance (Sep 30, 2019)
7-100155414-G-A			Likely benign (Aug 01, 2023)
7-100155498-A-G		Microcephaly 25, primary, autosomal recessive	Benign (Jul 14, 2021)
7-100155801-C-T		TRAPPC14-related disorder	Likely benign (May 10, 2022)
7-100156720-C-T		TRAPPC14-related disorder	Likely benign (Jun 05, 2019)
7-100156949-G-A		not specified	Uncertain significance (Jun 11, 2021)
7-100157126-G-A		TRAPPC14-related disorder	Benign (Dec 31, 2019)
7-100157657-C-A		Microcephaly 25, primary, autosomal recessive	Pathogenic (Jul 14, 2023)
7-100157720-C-T		TRAPPC14-related disorder	Likely benign (Apr 01, 2023)
7-100158248-C-G		TRAPPC14-related disorder	Likely benign (Jun 05, 2020)
7-100158256-G-A			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAPPC14	protein_coding	protein_coding	ENST00000316937	11	4296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.181	0.819	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	205	316	0.649	0.0000192	3645
Missense in Polyphen		39	61.548	0.63365		624
Synonymous	-1.09	153	137	1.12	0.00000829	1278
Loss of Function	3.40	6	24.0	0.250	0.00000129	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.466
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.497
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: BC037034

Gene ontology

• Cellular component: microtubule organizing center;plasma membrane;intracellular membrane-bounded organelle