EXOC6B

exocyst complex component 6B, the group of Exocyst complex

Basic information

Region (hg38): 2:72175983-72826041

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 (Limited), 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 (170 variants)
• Inborn genetic diseases (32 variants)
• not specified (1 variants)
• Spondyloepimetaphyseal dysplasia with joint laxity, type 3 (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.

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				33	9	42
missense			75	4	2	81
nonsense	1	2	3			6
start loss						0
frameshift			3		1	4
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1	2			3
splice region			4	7	7	18
non coding			1	27	9	37
Total	1	3	85	64	21

Variants in EXOC6B

This is a list of pathogenic ClinVar variants found in the EXOC6B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-72179342-T-C		EXOC6B-related disorder	Benign/Likely benign (Jan 22, 2024)
2-72179343-G-A			Uncertain significance (Jul 24, 2022)
2-72179406-G-A			Uncertain significance (Mar 17, 2023)
2-72179418-G-A		not specified	Uncertain significance (Jan 04, 2022)
2-72179428-A-G			Likely benign (Jul 10, 2023)
2-72179431-C-T			Uncertain significance (May 17, 2022)
2-72179432-ATGT-A			Uncertain significance (Nov 22, 2022)
2-72179435-T-C		not specified	Uncertain significance (Apr 12, 2023)
2-72182906-C-A			Likely pathogenic (Jul 21, 2023)
2-72182913-G-A			Likely benign (Mar 02, 2023)
2-72184058-T-C			Benign (Jan 09, 2024)
2-72184060-G-A			Likely benign (Oct 13, 2023)
2-72184067-G-C			Likely benign (Jan 19, 2024)
2-72184073-A-T		EXOC6B-related disorder	Uncertain significance (Dec 28, 2023)
2-72184095-A-G		EXOC6B-related disorder	Likely benign (Dec 10, 2023)
2-72184110-C-T			Likely benign (Nov 28, 2022)
2-72184112-G-A			Uncertain significance (Aug 30, 2022)
2-72184159-C-A		EXOC6B-related disorder	Uncertain significance (Dec 28, 2023)
2-72184191-TA-T			Benign (Aug 04, 2023)
2-72184204-C-A			Likely benign (Sep 02, 2022)
2-72251103-T-TCTGATTGATATTTAATAATGTAATTTAATTAAAATATATTTA		Schizophrenia	Uncertain significance (Nov 11, 2022)
2-72334927-A-C			Likely benign (Aug 08, 2023)
2-72334938-A-G			Likely benign (Oct 13, 2023)
2-72334944-T-C			Uncertain significance (Nov 10, 2023)
2-72334947-T-C			Uncertain significance (Aug 04, 2023)

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

• 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

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