AFG1L

AFG1 like ATPase

Basic information

Region (hg38): 6:108294991-108526796

Previous symbols: [ "LACE1" ]

Links

ENSG00000135537 ∙ NCBI:246269 ∙ OMIM:617469 ∙ HGNC:16411 ∙ Uniprot:Q8WV93 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AFG1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFG1L 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						0
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in AFG1L

This is a list of pathogenic ClinVar variants found in the AFG1L region.

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

Position	Type	Phenotype	Significance	ClinVar
6-108295101-T-G		not specified	Uncertain significance (May 13, 2024)
6-108295117-C-T		not specified	Uncertain significance (Apr 14, 2023)
6-108295157-C-G		not specified	Uncertain significance (Sep 20, 2023)
6-108295165-G-T		not specified	Uncertain significance (Sep 16, 2021)
6-108295198-C-G		not specified	Uncertain significance (Mar 19, 2024)
6-108323840-C-T		not specified	Uncertain significance (Mar 02, 2023)
6-108323845-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-108323851-A-G		not specified	Likely benign (Feb 14, 2023)
6-108323852-T-A		not specified	Uncertain significance (Nov 17, 2022)
6-108323896-G-A		not specified	Uncertain significance (Oct 13, 2023)
6-108323903-A-G		not specified	Uncertain significance (Nov 07, 2023)
6-108324005-A-G		not specified	Uncertain significance (May 03, 2023)
6-108355654-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-108355670-G-A		not specified	Uncertain significance (May 11, 2022)
6-108355672-T-C		not specified	Uncertain significance (Apr 01, 2024)
6-108355705-A-G		not specified	Uncertain significance (Oct 06, 2022)
6-108355716-C-T		not specified	Uncertain significance (Feb 22, 2023)
6-108356765-C-G		not specified	Uncertain significance (Mar 06, 2023)
6-108356780-T-C		not specified	Uncertain significance (Jun 18, 2024)
6-108356795-G-A		not specified	Uncertain significance (Apr 24, 2023)
6-108366322-G-C		not specified	Uncertain significance (Sep 27, 2021)
6-108447221-G-T		not specified	Uncertain significance (Oct 12, 2021)
6-108447242-C-T		not specified	Uncertain significance (Jan 17, 2023)
6-108447257-G-A		not specified	Uncertain significance (Jun 21, 2023)
6-108447281-G-A		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFG1L	protein_coding	protein_coding	ENST00000368977	13	231902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.44e-9	0.874	125569	0	179	125748	0.000712

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.805	228	265	0.861	0.0000140	3145
Missense in Polyphen		66	77.44	0.85228		898
Synonymous	-1.35	117	99.9	1.17	0.00000565	899
Loss of Function	1.70	17	26.4	0.643	0.00000136	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00650	0.00650
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000329	0.000326
South Asian	0.000297	0.000294
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative mitochondrial ATPase. Plays a role in mitochondrial morphology and mitochondrial protein metabolism. Promotes degradation of excess nuclear-encoded complex IV subunits (COX4I1, COX5A and COX6A1) and normal activity of complexes III and IV of the respiratory chain (PubMed:26759378, PubMed:27323408). Mediates mitochondrial translocation of TP53 and its transcription-independent apoptosis in response to genotoxic stress (PubMed:27323408). {ECO:0000269|PubMed:26759378, ECO:0000269|PubMed:27323408}.

Recessive Scores

• pRec: 0.154

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.96

Haploinsufficiency Scores

• pHI: 0.0899
• hipred: N
• hipred_score: 0.204
• ghis: 0.453

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Afg1l

Zebrafish Information Network

• Gene name: afg1lb
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: hydrocephalic

Gene ontology

• Biological process: mitochondrial electron transport, cytochrome c to oxygen;mitochondrion organization;mitochondrial protein catabolic process
• Cellular component: cytoplasm;mitochondrion;mitochondrial membrane
• Molecular function: protein binding;ATP binding;ATPase activity