ATP6AP1L

ATPase H+ transporting accessory protein 1 like (pseudogene)

Basic information

Region (hg38): 5:82295449-82318300

Links

ENSG00000205464 ∙ NCBI:92270 ∙ ∙ HGNC:28091 ∙ Uniprot:Q52LC2 ∙ 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 ATP6AP1L gene.

• Inborn genetic diseases (10 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP6AP1L 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			9	4		13
Total	0	0	9	4	0

Variants in ATP6AP1L

This is a list of pathogenic ClinVar variants found in the ATP6AP1L region.

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

Position	Type	Phenotype	Significance	ClinVar
5-82305423-G-C		not specified	Uncertain significance (Sep 22, 2023)
5-82310165-T-C		not specified	Uncertain significance (Aug 05, 2023)
5-82312638-G-A			Likely benign (Feb 01, 2023)
5-82312697-A-G		not specified	Uncertain significance (Jun 17, 2024)
5-82312714-A-C		not specified	Uncertain significance (Feb 17, 2023)
5-82312744-T-C			Likely benign (Jan 01, 2023)
5-82312798-A-G		not specified	Uncertain significance (May 31, 2023)
5-82312817-C-T		not specified	Uncertain significance (Aug 02, 2022)
5-82312823-T-C		not specified	Uncertain significance (Jul 12, 2023)
5-82317998-A-G		not specified	Uncertain significance (May 15, 2024)
5-82318003-A-G			Likely benign (Nov 01, 2022)
5-82318049-G-A		not specified	Likely benign (Apr 22, 2022)
5-82318050-C-A		not specified	Uncertain significance (Jan 26, 2022)
5-82318085-G-A		not specified	Uncertain significance (Feb 21, 2024)
5-82318130-A-C		not specified	Uncertain significance (Aug 17, 2022)
5-82318194-C-T		not specified	Uncertain significance (Mar 24, 2023)
5-82318217-G-C		not specified	Uncertain significance (Jan 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP6AP1L	protein_coding	protein_coding	ENST00000380167	4	107516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0299	0.929	125712	1	33	125746	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.338	115	126	0.915	0.00000725	1437
Missense in Polyphen		27	29.857	0.9043		425
Synonymous	0.955	47	56.1	0.838	0.00000339	457
Loss of Function	1.76	4	10.0	0.400	5.77e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000163
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000179	0.000167
Middle Eastern	0.000168	0.000163
South Asian	0.0000420	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.279
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.51

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.145
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp6ap1l

Gene ontology

• Biological process: ATP hydrolysis coupled proton transport;regulation of cellular pH
• Cellular component: integral component of membrane;proton-transporting V-type ATPase, V1 domain;plasma membrane proton-transporting V-type ATPase complex
• Molecular function: proton-transporting ATP synthase activity, rotational mechanism;proton-transporting ATPase activity, rotational mechanism