AAGAB

alpha and gamma adaptin binding protein

Basic information

Region (hg38): 15:67200667-67255195

Links

ENSG00000103591 ∙ NCBI:79719 ∙ OMIM:614888 ∙ HGNC:25662 ∙ Uniprot:Q6PD74 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• palmoplantar keratoderma, punctate type 1A (Strong), mode of inheritance: AD
• palmoplantar keratoderma, punctate type 1A (Strong), mode of inheritance: AD
• palmoplantar keratoderma, punctate type 1A (Strong), mode of inheritance: AD
• punctate palmoplantar keratoderma type 1 (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Keratoderma, palmoplantar, punctate type IA	AD	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	Dermatologic	23000146; 23064416

ClinVar

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

• not provided (10 variants)
• Palmoplantar keratoderma, punctate type 1A (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AAGAB 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	5	6
missense			30	1	3	34
nonsense	6	1				7
start loss		1				1
frameshift	3	1				4
inframe indel						0
splice donor/acceptor (+/-2bp)		2	1			3
splice region	1					1
non coding				5	13	18
Total	9	5	31	7	21

Highest pathogenic variant AF is 0.0000461

Variants in AAGAB

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

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

Position	Type	Phenotype	Significance	ClinVar
15-67202584-T-C			Benign (Jun 18, 2021)
15-67202848-T-G		not specified	Uncertain significance (Jul 06, 2021)
15-67202852-A-G		not specified	Uncertain significance (Oct 13, 2023)
15-67203547-C-A		Palmoplantar keratoderma, punctate type 1A	Likely pathogenic (Sep 20, 2019)
15-67203547-C-T		Palmoplantar keratoderma, punctate type 1A	Uncertain significance (Nov 01, 2021)
15-67203564-T-G		not specified	Uncertain significance (May 17, 2023)
15-67203588-G-A		not specified	Uncertain significance (Jun 24, 2022)
15-67203610-T-C			Likely benign (Jul 25, 2023)
15-67203885-A-AT			Benign (Jun 18, 2021)
15-67204051-T-A		not specified	Uncertain significance (Aug 20, 2023)
15-67204086-C-A		Palmoplantar keratoderma, punctate type 1A	Likely pathogenic (Jan 26, 2022)
15-67204091-T-A			Uncertain significance (Nov 27, 2023)
15-67204104-T-TG			Pathogenic (Aug 10, 2023)
15-67204120-T-A			Benign (Mar 23, 2023)
15-67204142-A-G		not specified	Uncertain significance (May 18, 2023)
15-67208576-A-C		not specified	Uncertain significance (Apr 24, 2024)
15-67208576-A-G		not specified	Uncertain significance (Nov 18, 2022)
15-67208584-A-T			Uncertain significance (May 22, 2023)
15-67208595-T-C			Benign (Jan 15, 2024)
15-67208603-C-T		not specified	Conflicting classifications of pathogenicity (Jan 07, 2022)
15-67208608-C-T			Benign (Nov 18, 2023)
15-67208609-C-G		not specified	Uncertain significance (May 24, 2024)
15-67208610-G-A			Uncertain significance (Dec 04, 2022)
15-67208695-G-A		Palmoplantar keratoderma, punctate type 1A	Benign (Dec 05, 2021)
15-67209254-C-T			Benign (Nov 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AAGAB	protein_coding	protein_coding	ENST00000261880	10	54163

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.87e-7	0.819	124757	0	38	124795	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.877	197	165	1.19	0.00000773	2064
Missense in Polyphen		77	62.563	1.2308		816
Synonymous	-0.546	66	60.6	1.09	0.00000301	591
Loss of Function	1.44	13	19.9	0.652	0.00000102	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000375	0.000375
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000111
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000239	0.000230
Middle Eastern	0.000112	0.000111
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in endocytic recycling of growth factor receptors such as EGFR. {ECO:0000269|PubMed:23064416}.

Intolerance Scores

• loftool: 0.751
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.321
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aagab

Gene ontology

• Biological process: protein transport
• Cellular component: cytoplasm;cytosol;nuclear speck
• Molecular function: protein binding