AFG2B

AFG2 AAA ATPase homolog B, the group of AAA ATPases

Basic information

Region (hg38): 15:45402336-45421415

Previous symbols: [ "SPATA5L1" ]

Links

ENSG00000171763 ∙ NCBI:79029 ∙ OMIM:619578 ∙ HGNC:28762 ∙ Uniprot:Q9BVQ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with hearing loss and spasticity (Moderate), mode of inheritance: AR
• hearing loss, autosomal recessive 119 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 119; Neurodevelopmental disorder with hearing loss and spasticity	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	34626583

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AFG2B gene.

• SPATA5L1-associated disorder (2 variants)
• Neurodevelopmental disorder with hearing loss and spasticity (1 variants)
• not provided (1 variants)
• Hearing loss, autosomal recessive 119 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFG2B 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				4	3	7
missense		8	57	1	3	69
nonsense	1					1
start loss			1			1
frameshift	2	1				3
inframe indel			2			2
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding					1	1
Total	4	9	60	5	7

Highest pathogenic variant AF is 0.00000658

Variants in AFG2B

This is a list of pathogenic ClinVar variants found in the AFG2B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-45402405-C-T			Benign (Jun 26, 2018)
15-45402430-A-T			Uncertain significance (Feb 05, 2018)
15-45402455-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jul 01, 2024)
15-45402466-C-G		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
15-45402503-G-T		Inborn genetic diseases	Uncertain significance (May 24, 2023)
15-45402505-A-G			Uncertain significance (Jul 23, 2021)
15-45402511-C-T			Uncertain significance (Mar 28, 2023)
15-45402514-T-G		See cases	Likely pathogenic (-)
15-45402524-G-A		Neurodevelopmental disorder with hearing loss and spasticity	Uncertain significance (Jan 27, 2024)
15-45402549-C-T		AFG2B-related disorder	Likely benign (Feb 24, 2022)
15-45402565-G-A		Inborn genetic diseases	Uncertain significance (Nov 03, 2022)
15-45402570-G-T			Benign (Jun 26, 2018)
15-45402619-C-T		Neurodevelopmental disorder with hearing loss and spasticity	Likely pathogenic (Aug 27, 2021)
15-45402620-G-A			Uncertain significance (Jun 18, 2020)
15-45402625-G-T			Uncertain significance (Jul 23, 2021)
15-45402642-T-G		Neurodevelopmental disorder with hearing loss and spasticity	Uncertain significance (May 12, 2023)
15-45402665-C-T		Inborn genetic diseases	Uncertain significance (May 02, 2024)
15-45402670-C-T		Inborn genetic diseases	Uncertain significance (May 23, 2023)
15-45402673-G-A		Inborn genetic diseases	Uncertain significance (Jun 16, 2023)
15-45402676-G-A		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
15-45402739-T-C			Uncertain significance (Sep 01, 2023)
15-45402805-C-G		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
15-45402817-G-A		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)
15-45402818-C-T		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)
15-45402832-G-A		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFG2B	protein_coding	protein_coding	ENST00000305560	8	19089

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.55e-11	0.508	125636	0	112	125748	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.861	346	394	0.878	0.0000190	4685
Missense in Polyphen		94	115.98	0.81051		1376
Synonymous	0.480	162	170	0.953	0.00000872	1691
Loss of Function	1.28	20	27.2	0.735	0.00000158	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000968	0.000958
Ashkenazi Jewish	0.000993	0.000993
East Asian	0.000989	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000410	0.000404
Middle Eastern	0.000989	0.000979
South Asian	0.000266	0.000261
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0896

Intolerance Scores

• loftool: 0.211
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.54

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.295
• ghis: 0.476

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata5l1

Gene ontology

• Cellular component: cytoplasm
• Molecular function: ATP binding;ATPase activity