AtlasGene
ATP6V1E1
ATPase H+ transporting V1 subunit E1
- HGNC 857↗(opens in a new tab)
- Ensembl gene ENSG00000131100↗(opens in a new tab)
- NCBI Gene 529↗(opens in a new tab)
Summary
- Cytogenetic location
- 22q11.21
- Coordinates
- Chromosome 22: 17,592,136–17,628,749 (GRCh38)
- Exons
- 9 exons across 36.6 kb
- Protein
- 226 amino acids
- Also known as
- P31, Vma4, ATP6E2
- Previous symbols
- ATP6E, ATP6V1E
- MANE Select transcript
- ENST00000253413.10NM_001696.4
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
AtlasThis page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
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page <- fromJSON(url)
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Get my Genome TestCurated report relevant to this gene
Cutis Laxa
Cutis laxa (CL) is an inherited or acquired connective tissue disorder characterized by wrinkled, redundant and sagging inelastic skin associated with skeletal and developmental anomalies and, in some cases, with severe systemic involvement. Several different forms of inherited CL have been described, differentiated on the basis of the mode of inheritance and differences in the extent of internal organ involvement, associated anomalies and disease severity.
- 3 GenCC submitters rate it definitive or strong
How ATP6V1E1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 1.3 kb of the gene's 36.6 kb; 681 of those bases code for the protein.
Sequencing ATP6V1E1
11Easy
How hard ATP6V1E1 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of ATP6V1E1's exons sit where short reads map cleanly.
What adds to it: the share of ATP6V1E1's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 100%.11%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 60%.0%
- Shared with chrYThe pseudoautosomal regions and the X-transposed region, where chrX and chrY carry the same or nearly the same sequence, so reads from either may land on the other. Weight 60%.0%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 50%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 30%.0.1%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 20%.2.6%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of ATP6V1E1's exon bases in that kind of difficult region. Any one kind can make a gene hard on its own, and each further kind adds less: 0 when no base is in any, 100 when every base is where reads cannot be placed uniquely.
1
position in ATP6V1E1 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 36.6 kb of ATP6V1E1, introns included, not only the 1.3 kb of exons.
ClinVar pathogenic variants (1)
The ATP6V1E1 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic/likely pathogenic 1
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_001696.4(ATP6V1E1):c.634C>T (p.Arg212Trp) (opens in a new tab) | autosomal recessive cutis laxa type 2C and 1 other | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
Genes linked to the same conditions
- ALDH18A1aldehyde dehydrogenase 18 family member A1Shares 1 condition
- ATP6V0A2ATPase H+ transporting V0 subunit a2Shares 1 condition
- ATP6V1AATPase H+ transporting V1 subunit AShares 1 condition
- ATP7AATPase copper transporting alphaShares 1 condition
- EFEMP1EGF-like fibulin extracellular matrix protein 1Shares 1 condition
- EFEMP2EGF-like fibulin extracellular matrix protein 2Shares 1 condition
- ELNelastinShares 1 condition
- EMILIN1elastin microfibril interfacer 1Shares 1 condition
- FBLN5fibulin 5Shares 1 condition
- GORABgolgin, RAB6 interactingShares 1 condition
- LTBP1latent transforming growth factor beta binding protein 1Shares 1 condition
- LTBP4latent transforming growth factor beta binding protein 4Shares 1 condition
Traits linked to ATP6V1E1
The Human Phenotype Ontology lists these as features of the rare conditions ATP6V1E1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of head or neck
- Beaked nose
- Central cleft palate
- Delayed closure of the soft spot on the skull
- Dental crowding
- Eyelid folded in
- Fullness around the eyes
- Long philtrum
- Narrow opening between the eyelids
Show 23 more traits
- Nasal tip, upturned
- Pointed chin
- Premature sagging cheeks
- Small forehead
- Triangular face
- Wide nasal base
- Broad nasal tip
- Deep laugh lines
- Dental cavities
- Downward slanting of the opening between the eyelids
- High palate
- Progressively abnormally small cranium
- Redundant neck skin
- Short nose
- Smooth philtrum
- Zygomatic flattening
- Big lower jaw
- Boxer's nasal deformity
- Dandy-Walker malformation
- Decreased size of maxilla
- Narrow mouth
- Broad columella
- Collapsed nostrils
Abnormality of the integument
- Abnormal fat tissue distribution below the skin
- Coarse hair
- Excessive wrinkled skin
- Fragmented elastic fibers in the dermis
- Hanging skin
- Loose redundant skin
- Sparse hair
- Thick hair
Show 1 more trait
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-19: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.19-9814e911.
Cite this page
Dante Labs. (n.d.). ATP6V1E1 gene: ATPase H+ transporting V1 subunit E1. Retrieved 19 October 2026, from https://dantelabs.com/genes/atp6v1e1
Dante Labs. ATP6V1E1 gene: ATPase H+ transporting V1 subunit E1 [Internet]. [cited 19 October 2026]. Available from: https://dantelabs.com/genes/atp6v1e1
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