ClinGen Dosage Sensitivity Curation Page

ACSL4

  • Curation Status: Complete

Location Information

Select assembly: (NC_000023.10) (NC_000023.11)
Evidence for haploinsufficiency phenotype
PubMed ID Description
11889465 Meloni (2002): The authors analyzed 12 individuals with intellectual disability and linkage between Xq21 and Xq26. Specifically, they sequenced 4 genes, including ACSL4 (referred to in this paper as FACL4) that lie in a 380kb critical region associated with intellectual disability only (as opposed to the contiguous gene syndrome that also includes features of Alport syndrome, caused by deletions in the Xq22.3 region). They identified a missense variant (p. (Arg529Ser)) in one individual, T22. T22 is part of a family with two other affected males (not counting T22), an affected female, and three female carriers who have transmitted the allele to an affected offspring. All carrier females for whom the assay was informative were said to have skewed X-inactivation. The authors then sequenced an additional 107 unrelated males with X-linked intellectual disability and identified another ACSL4 variant in individual P55. P55 and his two affected brothers were found to have a cryptic splice site variant (c.1003-2A>G) predicted to result in a stop codon, truncated protein and reduced enzyme activity. The carrier mother was normal and had skewed X-inactivation (Fig 2b). The authors note that ACSL4 encodes long-chain acyl-CoA synthetase type 4. Acyl-CoA synthetases catalyze the formation of acyl-CoA esters from fatty acids, ATP, and coenzyme A, and ACSL4 in particular is expressed in lymphocytes and has a "high substrate preference for arachidonic acid." Using this information, the authors tested enzyme activity in lymphoblastoid cell lines from individuals T22 and P55, an unrelated male with a larger deletion including ACSL4 and other genes (the contiguous gene syndrome mentioned above), the mother of the individual with the contiguous gene syndrome, and three controls. The authors demonstrated an 88%, 80%, and 86% reduction in enzyme levels (with respect to the normal controls) from the individual with the contiguous gene syndrome, T22, and P55, respectively. The carrier mother was shown to have normal enzyme activity (Figure 4).
12525535 Longo (2003) et al. evaluated 8 families with intellectual disability and linkage encompassing Xq22.3. In one of these families (MRX68), a missense variant was identified by direct Sanger sequencing of the coding sequence of ACSL4, changing a highly conserved proline into a leucine (p.P375L) in the luciferase domain. This variant was detected in 4 affected males with intellectual disability (a fifth reportedly affected male was deceased and unavailable for testing), and two female carriers that went on to have affected sons. A third female was assumed to be an obligate carrier based on her position in the pedigree (having an affected brother and an affected son). Enzymatic activity, specifically arachidonyl-CoA synthetase activity, was measured in lymphoblastoid and leukocytes from whole blood from one of the affected males in the family relative to controls (in this instance, other individuals affected with intellectual disability for whom no variants in ACSL4 were identified) as well as an individual with a large deletion including the ACSL4 (see Fig. 5). Arachidonyl-CoA synthetase activity (nmol/mg) was shown to be substantially decreased compared to the controls, and comparable to that of the reduction observed in the individual with the deletion. Enzymatic activity was not completely abolished in either the proband with the missense variant or the proband with the deletion.
21584729 Yonath et al. (2011) describe a 4th family with the missense variant, p.P375L, reported previously by Longo et al. in 2003, as described above. This Ashkenazi Jewish family included five males with intellectual disability, including the proband, and was initially studied via linkage analysis. Four of these affected males, including the proband, were found to have the "carrier haplotype"; one affected male was unavailable for testing. A male cousin of the proband (on the maternal side, the same side as the other affected relatives) was also found to have the carrier haplotype; this individual was said to have normal development, but was diagnosed with schizophrenia at 18 years of age. The linkage interval identified by the authors contained 192 known genes, including 9 that were reported in other individuals with intellectual disability at the time, but the authors only chose to sequence 3 genes that had previously been shown to result in skewed X-inactivation in females (including ACSL4), as the female carriers in the family exhibited skewed X-inactivation. The authors did not specify who in the pedigree was found to have the ACSL4 variant; it is unclear whether only the proband had sequencing once the linkage interval was identified, or if they went back and confirmed the presence of the variant in all individuals with the carrier haplotype. No enzyme assay was performed.
31481330 Chang et al. (2019) describe a 5th family w/ maternally inherited 9.75-kb deletion in a male detected on microarray and includes exons 1-6 of ACSL4. The proband was said to have early normal development, but presented with acute-onset left hemiparesis due to acute arterial ischemic stroke (which maybe incidental) at 16 months of age. At 3 years of age, severe communication delays were evident and behavioral difficulties included frequent outbursts, irritability, and tantrums were also noted. At 5 years of age, he was described as having "severely delayed language, intellectual, social, and behavioral development." The mom was observed to be mildly affected with a mosaic heterozygous deletion in the same region as the proband. No enzyme assay was performed.
26350204 Grozeva et al. (2015) report one proband (family 6) with a stop gain alteration, p.Arg654*, in exon 16 of 17 (variant occurs in last 50 bp of the second to last exon). Inheritance info not provided. It is indicated by the authors that ACSL4 is a known ID gene per "in-house curation" and the variant observed, NM_022977.2(ACSL4):c.1960C>T, was classified as "likely pathogenic." This variant was identified after performing a next-generation sequencing panel of 565 intellectual disability genes on a cohort of individuals with moderate-to-severe intellectual disability. No individual details about the proband were provided.
22581936

Haploinsufficiency phenotype comments:

Additional information includes: Hu et al. (2016) (PMID: 25644381) describe "massively parallel sequencing of all X-chromosome exons in the index males" of over 400 families with "unsolved" X-linked intellectual disability. The authors report the p.Arg654* variant (first reported in Grozeva et al. 2015, as described above) in a single family (Supplementary Table 5). No individual details on the proband are provided, though information from the Supplemental Material suggests there may be 7 affected males in this family. The authors do not mention that this variant was also observed in the Grozeva paper, and, based on the limited information in both papers (and at least one common author), it is unclear whether this represents two separate observations or the same family reported twice. Large deletions involving ACSL4 in addition to other genes have been reported, but were not considered in the overall evaluation of this gene due to the presence of other genes (PMIDs: 20186809, 16276108, 9598718, etc.). While there are several cases of variants in ACSL4 reported in families with X-linked intellectual disability, the evidence that variation in this gene is truly the cause of that intellectual disability is inconclusive at this time. The initial reports identified prospective families based on linkage studies, but did not fully interrogate the linkage regions to rule out other possible causes. While enzyme assays suggest that the reported missense variants have similar effects on enzyme activity as putative null variants, it is unclear whether lack of this enzyme truly results in a demonstrable phenotype. At least one reported nonsense variant is not expected to undergo nonsense-mediated decay, and no functional studies were performed to determine the effect of this variant. The pathogenicity of loss of function variants in ACSL4 is uncertain at this time, given that the role of ACSL4 as a potential cause of intellectual disability is also unclear.

The loss-of-function and triplosensitivity ratings for genes on the X chromosome are made in the context of a male genome to account for the effects of hemizygous duplications or nullizygous deletions. In contrast, disruption of some genes on the X chromosome causes male lethality and the ratings of dosage sensitivity instead take into account the phenotype in female individuals. Factors that may affect the severity of phenotypes associated with X-linked disorders include the presence of variable copies of the X chromosome (i.e. 47,XXY or 45,X) and skewed X-inactivation in females.

  • Triplosensitivity score: 0
  • Strength of Evidence (disclaimer): No evidence for dosage pathogenicity

The loss-of-function and triplosensitivity ratings for genes on the X chromosome are made in the context of a male genome to account for the effects of hemizygous duplications or nullizygous deletions. In contrast, disruption of some genes on the X chromosome causes male lethality and the ratings of dosage sensitivity instead take into account the phenotype in female individuals. Factors that may affect the severity of phenotypes associated with X-linked disorders include the presence of variable copies of the X chromosome (i.e. 47,XXY or 45,X) and skewed X-inactivation in females.