EXOC6B

exocyst complex component 6B, the group of Exocyst complex

Basic information

Region (hg38): 2:72175984-72826041

Previous symbols: [ "SEC15L2", "SEC15B" ]

Links

ENSG00000144036

∙ NCBI:23233 ∙ OMIM:607880 ∙ HGNC:17085 ∙ Uniprot:Q9Y2D4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

spondyloepimetaphyseal dysplasia with joint laxity (Supportive), mode of inheritance: AR
spondyloepimetaphyseal dysplasia with joint laxity, type 3 (Strong), mode of inheritance: AR
spondyloepimetaphyseal dysplasia with joint laxity, type 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spondyloepimetaphyseal dysplasia with joint laxity 3	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	Musculoskeletal	26669664; 30284759

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EXOC6B gene.

not_provided (218 variants)
not_specified (89 variants)
EXOC6B-related_disorder (16 variants)
Spondyloepimetaphyseal_dysplasia_with_joint_laxity,_type_3 (7 variants)
Schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOC6B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015189.3. 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			1 clinvar	52 clinvar	8 clinvar	61
missense			125 clinvar	5 clinvar	1 clinvar	131
nonsense	4 clinvar	2 clinvar	3 clinvar			9
start loss			1			1
frameshift	1 clinvar	2 clinvar	1 clinvar			4
splice donor/acceptor (+/-2bp)		4 clinvar	1 clinvar			5
Total	5	8	132	57	9

Highest pathogenic variant AF is 0.00000440155

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXOC6B	protein_coding	protein_coding	ENST00000272427	22	650058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.117	0.883	124616	0	22	124638	0.0000883

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	299	419	0.713	0.0000218	5326
Missense in Polyphen		98	176.29	0.5559		2324
Synonymous	0.946	136	151	0.902	0.00000790	1449
Loss of Function	4.90	12	49.1	0.245	0.00000278	575

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000659	0.000611
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.0000361	0.0000354
Middle Eastern	0.000169	0.000167
South Asian	0.000140	0.000131
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.;

Recessive Scores

pRec: 0.111

Intolerance Scores

loftool
rvis_EVS: -0.87
rvis_percentile_EVS: 10.8

Haploinsufficiency Scores

pHI: 0.598
hipred: Y
hipred_score: 0.651
ghis: 0.559

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.208

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Exoc6b
Phenotype

Gene ontology

Biological process: exocytosis;Golgi to plasma membrane transport;vesicle docking involved in exocytosis;protein transport
Cellular component: exocyst;membrane
Molecular function: protein binding